cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Cloning.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.model.molecular;
  10
  11 import javax.persistence.Column;
  12 import javax.persistence.Entity;
  13 import javax.persistence.FetchType;
  14 import javax.persistence.ManyToOne;
  15 import javax.xml.bind.annotation.XmlAccessType;
  16 import javax.xml.bind.annotation.XmlAccessorType;
  17 import javax.xml.bind.annotation.XmlElement;
  18 import javax.xml.bind.annotation.XmlIDREF;
  19 import javax.xml.bind.annotation.XmlRootElement;
  20 import javax.xml.bind.annotation.XmlSchemaType;
  21 import javax.xml.bind.annotation.XmlType;
  22
  23 import org.apache.log4j.Logger;
  24 import org.hibernate.envers.Audited;
  25 import org.hibernate.search.annotations.Field;
  26
  27 import eu.etaxonomy.cdm.model.common.EventBase;
  28 import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
  29 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  30
  31 /**
  32  * Cloning is a method used in {@link Amplification DNA amplification} for multiplying the base
  33  * material. Various cloning methods exist. Classical cloning methods use bacteria for cloning
  34  * while the latest approaches use other techniques.
  35  *
  36  * @author a.mueller
  37  * @since 2013-07-11
  38  *
  39  */
  40 @XmlAccessorType(XmlAccessType.FIELD)
  41 @XmlType(name = "Cloning", propOrder = {
  42         "strain",
  43         "forwardPrimer",
  44         "reversePrimer"
  45 })
  46 @XmlRootElement(name = "Cloning")
  47 @Entity
  48 @Audited
  49 public class Cloning extends MaterialOrMethodEvent implements Cloneable{
  50         private static final long serialVersionUID = 6179007910988646989L;
  51         @SuppressWarnings("unused")
  52         private static final Logger logger = Logger.getLogger(Cloning.class);
  53
  54         /** @see #getStrain() */
  55     @XmlElement(name = "strain")
  56         @Field
  57     @Column(length=100)
  58         private String strain;
  59
  60     /** @see #getForwardPrimer() */
  61     @XmlElement(name = "ForwardPrimer")
  62     @XmlIDREF
  63     @XmlSchemaType(name = "IDREF")
  64     @ManyToOne(fetch=FetchType.LAZY)
  65     private Primer forwardPrimer;
  66
  67     /** @see #getReversePrimer()*/
  68     @XmlElement(name = "ReversePrimer")
  69     @XmlIDREF
  70     @XmlSchemaType(name = "IDREF")
  71     @ManyToOne(fetch=FetchType.LAZY)
  72     private Primer reversePrimer;
  73
  74
  75 // ******************** FACTORY METHOD ******************/
  76
  77     public static Cloning NewInstance(){
  78         return new Cloning();
  79     }
  80
  81     public static Cloning NewInstance(DefinedTerm definedMaterialOrMethod, String methodText, String strain, Primer forwardPrimer, Primer reversePrimer){
  82         return new Cloning(definedMaterialOrMethod, methodText, strain, forwardPrimer, reversePrimer);
  83     }
  84
  85 // ********************* CONSTRUCTOR ********************/
  86
  87
  88     //made protected to fix a java.lang.InstantiationException which occurred while loading
  89     //see https://stackoverflow.com/questions/7273125/hibernate-envers-and-javassist-enhancement-failed-exception
  90     protected Cloning(){};
  91     protected Cloning(DefinedTerm definedMaterialOrMethod, String methodText, String strain, Primer forwardPrimer, Primer reversePrimer){
  92         super(definedMaterialOrMethod, methodText);
  93         this.strain = strain;
  94         this.forwardPrimer = forwardPrimer;
  95         this.reversePrimer = reversePrimer;
  96     }
  97
  98 // ********************* GETTER / SETTER ********************/
  99
 100
 101         /**
 102          * The primer used for forward cloning.
 103          * @see #getReversePrimer()
 104          */
 105         public Primer getForwardPrimer() {
 106                 return forwardPrimer;
 107         }
 108
 109         /**
 110          * @see #getForwardPrimer()
 111          * @see #getReversePrimer()
 112          */
 113         public void setForwardPrimer(Primer forwardPrimer) {
 114                 this.forwardPrimer = forwardPrimer;
 115         }
 116
 117         /**
 118          * The primer used for reverse cloning.
 119          * @see #getForwardPrimer()
 120          */
 121         public Primer getReversePrimer() {
 122                 return reversePrimer;
 123         }
 124
 125         /**
 126          * @see #getReversePrimer()
 127          * @see #getForwardPrimer()
 128          */
 129         public void setReversePrimer(Primer reversePrimer) {
 130                 this.reversePrimer = reversePrimer;
 131         }
 132
 133         public String getStrain() {
 134                 return strain;
 135         }
 136
 137         public void setStrain(String strain) {
 138                 this.strain = strain;
 139         }
 140
 141 // ********************* CLONE ********************/
 142         /**
 143          * Clones <i>this</i> {@link Cloning}. This is a shortcut that enables to create
 144          * a new instance that differs only slightly from <i>this</i> cloning by
 145          * modifying only some of the attributes.<BR><BR>
 146          *
 147          *
 148          * @see EventBase#clone()
 149          * @see java.lang.Object#clone()
 150          */
 151         @Override
 152         public Object clone()  {
 153                 Cloning result = (Cloning)super.clone();
 154
 155                 //don't change strain, forwardPrimer, backwardPrimer
 156                 return result;
 157         }
 158 }