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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.molecular;
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import java.util.HashSet;
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import java.util.Set;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.ManyToOne;
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import javax.persistence.OneToMany;
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import javax.persistence.Transient;
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import javax.validation.constraints.NotNull;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlElement;
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import javax.xml.bind.annotation.XmlElementWrapper;
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import javax.xml.bind.annotation.XmlIDREF;
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import javax.xml.bind.annotation.XmlRootElement;
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import javax.xml.bind.annotation.XmlSchemaType;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import org.hibernate.annotations.Cascade;
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import org.hibernate.annotations.CascadeType;
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import org.hibernate.envers.Audited;
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import org.hibernate.search.annotations.IndexedEmbedded;
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import eu.etaxonomy.cdm.model.occurrence.Collection;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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import eu.etaxonomy.cdm.strategy.cache.occurrence.DnaSampleDefaultCacheStrategy;
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/**
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* A DNA Sample is the extracted DNA of a given tissue sample. It may be stored in
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* a DNA Bank and should then be handled as a collection unit.
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* DNA Sample are used to determine their {@link Sequence DNA sequences}
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* starting with a process called {@link Amplification amplification}.
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*
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* @author m.doering
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* @since 08-Nov-2007
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "DnaSample", propOrder = {
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"sequences",
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"amplificationResults",
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"dnaQuality"
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})
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@XmlRootElement(name = "DnaSample")
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@Entity
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//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
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//@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
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@Audited
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public class DnaSample extends DerivedUnit {
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private static final long serialVersionUID = -2978411330023671805L;
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@SuppressWarnings("unused")
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private static final Logger logger = LogManager.getLogger(DnaSample.class);
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// ****************** FACTORY METHOD *****************/
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public static DnaSample NewInstance(){
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return new DnaSample(SpecimenOrObservationType.DnaSample);
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}
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public static DnaSample NewTissueSampleAsDnaSampleInstance(){
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return new DnaSample(SpecimenOrObservationType.TissueSample);
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}
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// ************** ATTRIBUTES ****************************/
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@XmlElementWrapper(name = "Sequences")
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@XmlElement(name = "sequence")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@OneToMany(mappedBy="dnaSample", fetch = FetchType.LAZY)
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@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
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private Set<Sequence> sequences = new HashSet<>();
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@XmlElementWrapper(name = "AmplificationResults")
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@XmlElement(name = "AmplificationResult")
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@OneToMany(mappedBy="dnaSample", fetch = FetchType.LAZY)
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@Cascade( { CascadeType.SAVE_UPDATE,CascadeType.MERGE, CascadeType.DELETE})
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@NotNull
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private final Set<AmplificationResult> amplificationResults = new HashSet<>();
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@XmlElement(name = "DnaQuality", required = true)
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToOne(fetch = FetchType.LAZY)
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@IndexedEmbedded
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
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private DnaQuality dnaQuality;
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// ******************* CONSTRUCTOR *************************/
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//for hibernate use only, *packet* private required by bytebuddy
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@Deprecated
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DnaSample() {}
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private DnaSample(SpecimenOrObservationType type) {
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super(type);
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}
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@Override
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protected void initDefaultCacheStrategy() {
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if (this.getRecordBasis() == null || SpecimenOrObservationType.DnaSample.equals(this.getRecordBasis())){
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this.cacheStrategy = new DnaSampleDefaultCacheStrategy();
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}else{
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super.initDefaultCacheStrategy();
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}
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}
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//************ GETTER / SETTER **********************************/
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//sequencings
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public Set<Sequence> getSequences() {
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return sequences;
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}
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public void addSequence(Sequence sequence) {
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if (sequence.getDnaSample() != null){
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sequence.getDnaSample().removeSequence(sequence);
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}
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this.sequences.add(sequence);
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sequence.setDnaSample(this);
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}
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public void removeSequence(Sequence sequence) {
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sequence.setDnaSample(null);
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this.sequences.remove(sequence);
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}
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//amplifications
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public Set<AmplificationResult> getAmplificationResults() {
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return amplificationResults;
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}
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public void addAmplificationResult(AmplificationResult amplificationResult) {
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this.amplificationResults.add(amplificationResult);
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amplificationResult.setDnaSample(this);
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}
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public void removeAmplificationResult(AmplificationResult amplificationResult) {
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this.amplificationResults.remove(amplificationResult);
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amplificationResult.setDnaSample(null);
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}
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public DnaQuality getDnaQuality() {
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return dnaQuality;
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}
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public void setDnaQuality(DnaQuality dnaQuality) {
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this.dnaQuality = dnaQuality;
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}
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// ************* Convenience Getter / Setter ************/
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@Transient
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public Collection getStoredAt(){
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return this.getCollection();
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}
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public void setStoredAt(Collection storedAt){
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this.setCollection(storedAt);
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}
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@Transient
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public Set<SpecimenOrObservationBase> getExtractedFrom(){
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return getOriginals();
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}
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@Transient
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public String getBankNumber(){
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return this.getCatalogNumber();
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}
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public void setBankNumber(String bankNumber){
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this.setCatalogNumber(bankNumber);
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}
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//*********** CLONE **********************************/
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/**
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* Clones <i>this</i> dna sample. This is a shortcut that enables to
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* create a new instance that differs only slightly from <i>this</i> dna sample
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* by modifying only some of the attributes.<BR>
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* This method overrides the clone method from {@link Specimen Specimen}.
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* @throws CloneNotSupportedException
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*
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* @see Specimen#clone()
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* @see DerivedUnit#clone()
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* @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
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* @see java.lang.Object#clone()
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*/
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@Override
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public DnaSample clone() {
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DnaSample result = (DnaSample)super.clone();
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//sequenceSet
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result.sequences = new HashSet<>();
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for(Sequence sequence : this.sequences) {
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result.addSequence(sequence.clone());
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}
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//no changes to: bankNumber
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return result;
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}
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}
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