X-Git-Url: https://dev.e-taxonomy.eu/gitweb/cdmlib.git/blobdiff_plain/ffe91453485c0d649c4d8b2b34e4da49af683b4b..0f1568df9c2cccc7a1b037b7913a5b55cda41978:/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java
index fe11c1b4dd..2ef4788c93 100644
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaSample.java
@@ -17,6 +17,7 @@ import javax.persistence.Entity;
 import javax.persistence.FetchType;
 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;
@@ -30,32 +31,40 @@ import org.apache.log4j.Logger;
 import org.hibernate.annotations.Cascade;
 import org.hibernate.annotations.CascadeType;
 import org.hibernate.envers.Audited;
+import org.hibernate.search.annotations.ContainedIn;
 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.DerivedUnit;
 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
 import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
 
 /**
+ * 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
- * @version 1.0
- * @created 08-Nov-2007 13:06:22
+ * @created 08-Nov-2007
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "DnaSample", propOrder = {
-    "sequences"
+    "sequences",
+    "amplifications"
 })
 @XmlRootElement(name = "DnaSample")
 @Entity
 @Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
 @Audited
-public class DnaSample extends Specimen implements Cloneable {
+public class DnaSample extends DerivedUnit implements Cloneable {
 	private static final long serialVersionUID = -2978411330023671805L;
 	@SuppressWarnings("unused")
 	private static final Logger logger = Logger.getLogger(DnaSample.class);
 	
+// ****************** FACTORY METHOD *****************/
+	
 	/**
 	 * Factory method
 	 * @return
@@ -64,6 +73,7 @@ public class DnaSample extends Specimen implements Cloneable {
 		return new DnaSample();
 	}
 
+// ************** ATTRIBUTES ****************************/	
 	
 //	@XmlElement(name = "BankNumber")
 //	private String bankNumber;
@@ -77,29 +87,56 @@ public class DnaSample extends Specimen implements Cloneable {
     private Set<Sequence> sequences = new HashSet<Sequence>();
 
 	
+	@XmlElementWrapper(name = "Amplifications")
+	@XmlElement(name = "Amplification")
+	@OneToMany(mappedBy="dnaSample", fetch = FetchType.LAZY)
+	@Cascade( { CascadeType.SAVE_UPDATE, CascadeType.DELETE})
+    @ContainedIn
+    @NotNull
+	private Set<Amplification> amplifications = new HashSet<Amplification>();
+
+
+// ******************* CONSTRUCTOR *************************/
 	
 	/**
 	 * Constructor
 	 */
 	private DnaSample() {
-		super();
-		this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Specimen>();
+		super(SpecimenOrObservationType.DnaSample);
+		this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<DerivedUnit>();
 	}
 	
+//************ GETTER / SETTER  **********************************/	
+
+	//sequencings
 	public Set<Sequence> getSequences() {
 		return sequences;
 	}
 
-	// FIXME shouldn't this be the singular? i.e. addSequence( . . . )
-	public void addSequences(Sequence sequence) {
+	public void addSequence(Sequence sequence) {
 		this.sequences.add(sequence);
 	}
 
-	// FIXME shouldn't this be the singular? i.e. removeSequence( . . . )
-	public void removeSequences(Sequence sequence) {
+	public void removeSequence(Sequence sequence) {
 		this.sequences.remove(sequence);
 	}
+	
+	//amplifications
+	public Set<Amplification> getAmplifications() {
+		return amplifications;
+	}
 
+	public void addAmplification(Amplification amplification) {
+		this.amplifications.add(amplification);
+		amplification.setDnaSample(this);
+	}
+
+	public void removeAmplification(Amplification amplification) {
+		this.amplifications.remove(amplification);
+	}
+
+// ************* Convenience Getter / Setter ************/
+	
 	@Transient
 	public Collection getStoredAt(){
 		return this.getCollection();
@@ -131,19 +168,20 @@ public class DnaSample extends Specimen implements Cloneable {
 	 * 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 DerivedUnitBase#clone()
+	 * @see DerivedUnit#clone()
 	 * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
 	 * @see java.lang.Object#clone()
 	 */
 	@Override
-	public DnaSample clone(){
+	public DnaSample clone() {
 		DnaSample result = (DnaSample)super.clone();
 		//sequenceSet
 		result.sequences = new HashSet<Sequence>();
 		for(Sequence sequence : this.sequences) {
-			result.addSequences(sequence);
+			result.addSequence(sequence);
 		}
 		//no changes to: bankNumber
 		return result;