package eu.etaxonomy.cdm.model.molecular;
-import eu.etaxonomy.cdm.model.occurrence.Collection;
-import eu.etaxonomy.cdm.model.occurrence.Specimen;
-import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
-import org.apache.log4j.Logger;
+import java.util.HashSet;
+import java.util.Set;
-import java.util.*;
-
-import javax.persistence.*;
+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;
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.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.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 = {
- "bankNumber",
- "sequences"
+ "sequences",
+ "amplifications"
})
@XmlRootElement(name = "DnaSample")
@Entity
-public class DnaSample extends Specimen {
+@Indexed(index = "eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase")
+@Audited
+public class DnaSample extends DerivedUnit implements Cloneable {
+ private static final long serialVersionUID = -2978411330023671805L;
+ @SuppressWarnings("unused")
+ private static final Logger logger = Logger.getLogger(DnaSample.class);
- static Logger logger = Logger.getLogger(DnaSample.class);
+// ****************** FACTORY METHOD *****************/
- @XmlElement(name = "BankNumber")
- private String bankNumber;
+ /**
+ * Factory method
+ * @return
+ */
+ public static DnaSample NewInstance(){
+ return new DnaSample();
+ }
+
+// ************** ATTRIBUTES ****************************/
+
+// @XmlElement(name = "BankNumber")
+// private String bankNumber;
@XmlElementWrapper(name = "Sequences")
@XmlElement(name = "sequence")
- private Set<Sequence> sequences = new HashSet();
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @OneToMany(fetch = FetchType.LAZY)
+ @Cascade(CascadeType.SAVE_UPDATE)
+ 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>();
+
- @OneToMany
+// ******************* CONSTRUCTOR *************************/
+
+ /**
+ * Constructor
+ */
+ private DnaSample() {
+ super(SpecimenOrObservationType.DnaSample);
+ this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<DerivedUnit>();
+ }
+
+//************ GETTER / SETTER **********************************/
+
+ //sequencings
public Set<Sequence> getSequences() {
return sequences;
}
- protected void setSequences(Set<Sequence> sequences) {
- this.sequences = sequences;
- }
- public void addSequences(Sequence sequence) {
+
+ public void addSequence(Sequence sequence) {
this.sequences.add(sequence);
}
- 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();
}
+
public void setStoredAt(Collection storedAt){
this.setCollection(storedAt);
}
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<Sequence>();
+ for(Sequence sequence : this.sequences) {
+ result.addSequence(sequence);
+ }
+ //no changes to: bankNumber
+ return result;
+ }
}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff