cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Primer.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.annotations.Cascade;
  25 import org.hibernate.annotations.CascadeType;
  26 import org.hibernate.envers.Audited;
  27
  28 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  29 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  30 import eu.etaxonomy.cdm.model.reference.Reference;
  31
  32 /**
  33  * A primer is a (short) DNA Sequence used for replication and extraction
  34  * of DNA parts during e.g. {@link Amplification amplification} or
  35  * {@link SingleRead sequence reading}.
  36  *
  37  * @author a.mueller
  38  * @created 2013-07-08
  39  *
  40  */
  41 @XmlAccessorType(XmlAccessType.FIELD)
  42 @XmlType(name = "Primer", propOrder = {
  43         "label",
  44         "sequence",
  45         "dnaMarker",
  46         "publishedIn"
  47 })
  48 @XmlRootElement(name = "Primer")
  49 @Entity
  50 @Audited
  51 //TODO which base class  (..., identifiable, definedTerm, ...)
  52 public class Primer extends AnnotatableEntity {
  53         private static final long serialVersionUID = 6179007910988646989L;
  54         private static final Logger logger = Logger.getLogger(Primer.class);
  55
  56         /** @see #getLabel() */
  57         @XmlElement(name = "Label")
  58     @Column(length=255)
  59         private String label;
  60
  61         /** @see #getSequence() */
  62         //(see #4139)
  63         @XmlElement(name = "Sequence")
  64         private SequenceString sequence = SequenceString.NewInstance();
  65
  66
  67     /** @see #getDnaMarker()*/
  68     @XmlElement(name = "DnaMarker")
  69     @XmlIDREF
  70     @XmlSchemaType(name = "IDREF")
  71     @ManyToOne(fetch=FetchType.LAZY)
  72     private DefinedTerm dnaMarker;
  73
  74         /** @see #getPublishedIn() */
  75         @XmlElement(name = "PublishedIn")
  76     @XmlIDREF
  77     @XmlSchemaType(name = "IDREF")
  78     @ManyToOne(fetch=FetchType.LAZY)
  79     @Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE})
  80         private Reference<?> publishedIn;
  81
  82
  83
  84         // ******************** FACTORY METHOD ******************/
  85
  86         public static Primer NewInstance(String label){
  87                 Primer result = new Primer();
  88                 result.setLabel(label);
  89                 return result;
  90         }
  91
  92         // ********************* CONSTRUCTOR ********************/
  93
  94         //made protected to fix a java.lang.InstantiationException which occurred while loading an Amplification
  95         //and its primer. see https://stackoverflow.com/questions/7273125/hibernate-envers-and-javassist-enhancement-failed-exception
  96         protected Primer(){}
  97
  98 // ********************* GETTER / SETTER ********************/
  99
 100
 101         /**
 102          * The name of this primer, usually given by the producers.
 103          * @return the label of this primer.
 104          */
 105         public String getLabel() {
 106                 return label;
 107         }
 108
 109         /**
 110          * @see #getLabel()
 111          */
 112         public void setLabel(String label) {
 113                 this.label = label;
 114         }
 115
 116         /**
 117          * The DNA {@link Sequence} of this primer. A primer is usually a
 118          * small piece of DNA and therefore can be expressed as a sequence.
 119          */
 120         public SequenceString getSequence() {
 121                 return sequence;
 122         }
 123
 124         /**
 125          * @see Primer#getSequence()
 126          */
 127         public void setSequence(SequenceString sequence) {
 128                 if (sequence == null){
 129                         sequence = SequenceString.NewInstance();
 130                 }
 131                 this.sequence = sequence;
 132         }
 133
 134
 135         /**
 136          * #4470
 137          */
 138         public DefinedTerm getDnaMarker() {
 139                 return dnaMarker;
 140         }
 141
 142         public void setDnaMarker(DefinedTerm dnaMarker) {
 143                 this.dnaMarker = dnaMarker;
 144         }
 145
 146         /**
 147          * The reference in which this primer was published and described
 148          * for the first time. It is not a reference or citation for the
 149          * sequence of this primer.<BR>
 150          * Links to this reference are stored with the reference itself.
 151          * @return the describing publication of this primer
 152          */
 153         public Reference getPublishedIn() {
 154                 return publishedIn;
 155         }
 156
 157         /**
 158          * @see #getPublishedIn()
 159          */
 160         public void setPublishedIn(Reference publishedIn) {
 161                 this.publishedIn = publishedIn;
 162         }
 163
 164         // ********************* CLONE ********************/
 165         /**
 166          * Clones <i>this</i> primer. This is a shortcut that enables to create
 167          * a new instance that differs only slightly from <i>this</i> primer by
 168          * modifying only some of the attributes.<BR><BR>
 169          *
 170          *
 171          * @see eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
 172          * @see java.lang.Object#clone()
 173          */
 174         @Override
 175         public Object clone()  {
 176                 try{
 177                 Primer result = (Primer)super.clone();
 178
 179 //              don't change label, sequence
 180                 result.publishedIn = this.publishedIn;
 181
 182                 return result;
 183                 }catch (CloneNotSupportedException e) {
 184                         logger.warn("Object does not implement cloneable");
 185                         e.printStackTrace();
 186                         return null;
 187                 }
 188         }
 189 }