dna Quality purification method

[cdmlib.git] / cdmlib-model / src / main / java / eu / etaxonomy / cdm / model / molecular / DnaQuality.java

diff --git a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaQuality.java b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaQuality.java
index 7daa1eb6d310c5b9e6a82a9ca86bf819bfc72bb5..efec243b05b6bfce0c1ec0f96f5d1d4b1d427a27 100644 (file)
--- a/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaQuality.java
+++ b/cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/DnaQuality.java
@@ -1,8 +1,8 @@
 /**
 * Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy 
+* 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.
 */
@@ -33,15 +33,16 @@ import org.joda.time.DateTime;
 
 import eu.etaxonomy.cdm.hibernate.search.DateTimeBridge;
 import eu.etaxonomy.cdm.jaxb.DateTimeAdapter;
-import eu.etaxonomy.cdm.model.common.DefinedTerm;
+import eu.etaxonomy.cdm.model.common.OrderedTerm;
 import eu.etaxonomy.cdm.model.common.VersionableEntity;
 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
+import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
 
 /**
  * A DNA Quality describes the quality of a {@link SpecimenOrObservationType#DnaSample}
- *  
+ *
  * @author a.mueller
  * @created 18-Oct-2014
  */
@@ -63,9 +64,9 @@ public class DnaQuality extends VersionableEntity implements Cloneable {
        private static final long serialVersionUID = -8829069331010573654L;
        @SuppressWarnings("unused")
        private static final Logger logger = Logger.getLogger(DnaQuality.class);
-       
+
 // ****************** FACTORY METHOD *****************/
-       
+
        /**
         * Factory method
         * @return
@@ -74,34 +75,37 @@ public class DnaQuality extends VersionableEntity implements Cloneable {
                return new DnaQuality();
        }
 
-// ************** ATTRIBUTES ****************************/     
-    
+// ************** ATTRIBUTES ****************************/
+
     //TODO
-//    @XmlTransient
-//    @Transient
-//    private MaterialOrMethodEvent purificationMethod;
+//     @XmlElement(name = "PurificationMethod")
+//    @XmlIDREF
+//    @XmlSchemaType(name = "IDREF")
+//    @ManyToOne(fetch = FetchType.LAZY)
+//    private MaterialOrMethodEvent purificationMethodTerm;
+       
     private String purificationMethod;
 
-       
+
        private Double ratioOfAbsorbance260_230;
-       
+
        private Double ratioOfAbsorbance260_280;
-       
+
        private Double concentration;
 
-       @XmlElement(name = "Type")
+       @XmlElement(name = "concentrationUnit")
     @XmlIDREF
     @XmlSchemaType(name = "IDREF")
     @ManyToOne(fetch = FetchType.LAZY)
        private MeasurementUnit concentrationUnit;
-    
-       
+
+
        @XmlElement(name = "Type")
     @XmlIDREF
     @XmlSchemaType(name = "IDREF")
     @ManyToOne(fetch = FetchType.LAZY)
-       private DefinedTerm qualityTerm;
-    
+       private OrderedTerm qualityTerm;
+
     @XmlElement (name = "QualityCheckDate", type= String.class)
     @XmlJavaTypeAdapter(DateTimeAdapter.class)
     @Type(type="dateTimeUserType")
@@ -110,17 +114,17 @@ public class DnaQuality extends VersionableEntity implements Cloneable {
     @FieldBridge(impl = DateTimeBridge.class)
     @Audited
     private DateTime qualityCheckDate;
-    
+
 
 // ******************* CONSTRUCTOR *************************/
-       
+
        /**
         * Constructor
         */
-       private DnaQuality() {}
-       
-//************ GETTER / SETTER  **********************************/    
-       
+       protected DnaQuality() {}
+
+//************ GETTER / SETTER  **********************************/
+
 
        public String getPurificationMethod() {
                return purificationMethod;
@@ -145,8 +149,8 @@ public class DnaQuality extends VersionableEntity implements Cloneable {
        public void setRatioOfAbsorbance260_280(Double ratioOfAbsorbance260_280) {
                this.ratioOfAbsorbance260_280 = ratioOfAbsorbance260_280;
        }
-       
-       
+
+
     public Double getConcentration() {
                return concentration;
        }
@@ -171,24 +175,24 @@ public class DnaQuality extends VersionableEntity implements Cloneable {
                this.qualityCheckDate = qualityCheckDate;
        }
 
-       public DefinedTerm getQualityTerm() {
+       public OrderedTerm getQualityTerm() {
                return qualityTerm;
        }
 
-       public void setQualityTerm(DefinedTerm qualityTerm) {
+       public void setQualityTerm(OrderedTerm qualityTerm) {
                this.qualityTerm = qualityTerm;
        }
 
-       
 
-//*********** CLONE **********************************/        
-       
-       /** 
+
+//*********** CLONE **********************************/
+
+       /**
         * Clones <i>this</i> dna quality. This is a shortcut that enables to
         * create a new instance that differs only slightly from <i>this</i> dna quality
         * by modifying only some of the attributes.<BR>
-        * @throws CloneNotSupportedException 
-        * 
+        * @throws CloneNotSupportedException
+        *
         * @see Specimen#clone()
         * @see DerivedUnit#clone()
         * @see eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity#clone()
@@ -198,14 +202,14 @@ public class DnaQuality extends VersionableEntity implements Cloneable {
        public DnaQuality clone() {
                try {
                        DnaQuality result = (DnaQuality)super.clone();
-                       
+
                        //purification method ??
-                       
-                       //no changes to: rationXXX, concentration, qualityCheckDate, qualityTerm, 
+
+                       //no changes to: rationXXX, concentration, qualityCheckDate, qualityTerm,
                        return result;
-                       
+
                } catch (CloneNotSupportedException e) {
-                       throw new RuntimeException(e);  //may not occur as Clonable is implemented 
+                       throw new RuntimeException(e);  //may not occur as Clonable is implemented
                }
        }