cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Amplification.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.Entity;
  12 import javax.persistence.FetchType;
  13 import javax.persistence.JoinColumn;
  14 import javax.persistence.ManyToOne;
  15 import javax.validation.constraints.Size;
  16 import javax.xml.bind.annotation.XmlAccessType;
  17 import javax.xml.bind.annotation.XmlAccessorType;
  18 import javax.xml.bind.annotation.XmlElement;
  19 import javax.xml.bind.annotation.XmlIDREF;
  20 import javax.xml.bind.annotation.XmlRootElement;
  21 import javax.xml.bind.annotation.XmlSchemaType;
  22 import javax.xml.bind.annotation.XmlType;
  23
  24 import org.apache.log4j.Logger;
  25 import org.hibernate.annotations.Cascade;
  26 import org.hibernate.annotations.CascadeType;
  27 import org.hibernate.envers.Audited;
  28 import org.hibernate.search.annotations.Analyze;
  29 import org.hibernate.search.annotations.Field;
  30 import org.hibernate.search.annotations.IndexedEmbedded;
  31 import org.hibernate.search.annotations.NumericField;
  32
  33 import eu.etaxonomy.cdm.model.agent.Institution;
  34 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  35 import eu.etaxonomy.cdm.model.common.EventBase;
  36 import eu.etaxonomy.cdm.model.common.TermType;
  37 import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
  38
  39 /**
  40  * The physical process of amplification (also called PCR) extracts and replicates parts of the DNA of
  41  * a given {@link #getDnaSample() DNA Sample} . The part of the DNA being replicated is defined by the
  42  * {@link #getDnaMarker() marker} (also called locus) - implemented in CDM as a {@link DefinedTerm}
  43  * of term type {@link TermType#DnaMarker}.
  44  * <BR>To execute the replication {@link Primer primers} (short DNA fractions) are
  45  * used. They may work in both directions of the DNA part therefore we do have a
  46  * {@link #getForwardPrimer() forward primer} and a {@link #getReversePrimer() reverse primer}.
  47  * Most (or all?) amplifications require a {@link #getPurification() purification process}. Additionally
  48  * some use {@link #getCloning()} for replication.
  49  * <H3>Quality control</H3>
  50  * <BR>For quality control the resulting product (PCR) is tested using a chromatographic method called
  51  * electrophoresis. The parameters (voltage, ladder used, running time, and gel concentration) used
  52  * for this electrophoresis as well as the resulting
  53  * {@link #getGelPhoto() photo} can also be stored in the amplification instance.
  54  * <BR>The resulting PCR will later be used in a {@link SingleRead DNA sequence reading process}.
  55  * The PCR itself is not persistent and therefore will not be stored in the CDM.
  56  * This may change in future: http://dev.e-taxonomy.eu/trac/ticket/3717.
  57  * <BR>
  58  *
  59  * @author a.mueller
  60  * @created 2013-07-05
  61  *
  62  */
  63 @XmlAccessorType(XmlAccessType.FIELD)
  64 @XmlType(name = "Amplification", propOrder = {
  65         "dnaMarker",
  66         "forwardPrimer",
  67         "reversePrimer",
  68         "purification",
  69         "institution",
  70         "ladderUsed",
  71         "electrophoresisVoltage",
  72         "gelRunningTime",
  73         "gelConcentration",
  74 })
  75 @XmlRootElement(name = "Amplification")
  76 @Entity
  77 @Audited
  78 public class Amplification extends EventBase implements Cloneable{
  79         private static final long serialVersionUID = -6382383300974316261L;
  80
  81         private static final Logger logger = Logger.getLogger(Amplification.class);
  82
  83     /** @see #getDnaMarker()*/
  84     @XmlElement(name = "DnaMarker")
  85     @XmlIDREF
  86     @XmlSchemaType(name = "IDREF")
  87     //TODO why is this eager?
  88     @ManyToOne(fetch=FetchType.EAGER)
  89     private DefinedTerm dnaMarker;
  90
  91     /** @see #getForwardPrimer() */
  92     @XmlElement(name = "ForwardPrimer")
  93     @XmlIDREF
  94     @XmlSchemaType(name = "IDREF")
  95     @ManyToOne(fetch=FetchType.LAZY)
  96     @Cascade({CascadeType.SAVE_UPDATE})
  97     private Primer forwardPrimer;
  98
  99     /** @see #getReversePrimer()*/
 100     @XmlElement(name = "ReversePrimer")
 101     @XmlIDREF
 102     @XmlSchemaType(name = "IDREF")
 103     @ManyToOne(fetch=FetchType.LAZY)
 104     @Cascade({CascadeType.SAVE_UPDATE})
 105     private Primer reversePrimer;
 106
 107
 108     @XmlElement(name = "Purification")
 109     @XmlIDREF
 110     @XmlSchemaType(name = "IDREF")
 111     @ManyToOne(fetch=FetchType.LAZY)
 112     @Cascade({CascadeType.SAVE_UPDATE})
 113     private MaterialOrMethodEvent purification;
 114
 115         @XmlElement(name = "Institution")
 116         @XmlIDREF
 117         @XmlSchemaType(name = "IDREF")
 118         @ManyToOne(fetch = FetchType.LAZY)
 119         @IndexedEmbedded
 120         @Cascade(CascadeType.SAVE_UPDATE)
 121         @JoinColumn(name="institution_id")
 122         private Institution institution;
 123
 124     /** @see #getLadderUsed() */
 125     @XmlElement(name = "ladderUsed")
 126         @Field
 127         @Size(max=255)
 128         private String ladderUsed;
 129
 130     /** @see #getElectrophoresisVoltage()*/
 131         @XmlElement(name = "electrophoresisVoltage")
 132         @Field(analyze = Analyze.NO)
 133         @NumericField
 134         private Double electrophoresisVoltage;
 135
 136     /** @see #getGelRunningTime() */
 137         @XmlElement(name = "gelRunningTime")
 138         @Field(analyze = Analyze.NO)
 139         @NumericField
 140         private Double gelRunningTime;
 141
 142     /** @see #getGelConcentration() */
 143         @XmlElement(name = "gelConcentration")
 144         @Field(analyze = Analyze.NO)
 145         @NumericField
 146         private Double gelConcentration;
 147
 148
 149 // ********************* FACTORY METHODS ************************/
 150
 151         public static Amplification NewInstance(){
 152             return new Amplification();
 153         }
 154
 155
 156 // ******************* CONSTRUCTOR *******************************/
 157
 158         protected Amplification(){}
 159
 160
 161 //********************* GETTER / SETTER ************/
 162
 163
 164         /**
 165          * The {@link TermType#DnaMarker DNA marker} used for this amplification.
 166          * The DNA marker also defines the part (locality) of the DNA/RNA examined.
 167          * It may also be called <i>locus</i>
 168          */
 169         public DefinedTerm getDnaMarker() {
 170                 return dnaMarker;
 171         }
 172         /** @see #getDnaMarker()*/
 173         public void setDnaMarker(DefinedTerm marker) {
 174                 this.dnaMarker = marker;
 175         }
 176
 177         /**
 178          * The primer used for forward amplification.
 179          * @see #getReversePrimer()
 180          */
 181         public Primer getForwardPrimer() {
 182                 return forwardPrimer;
 183         }
 184         /**
 185          * @see #getForwardPrimer()
 186          * @see #getReversePrimer()
 187          */
 188         public void setForwardPrimer(Primer forwardPrimer) {
 189                 this.forwardPrimer = forwardPrimer;
 190         }
 191
 192         /**
 193          * The primer used for reverse amplification.
 194          * @see #getForwardPrimer()
 195          */
 196         public Primer getReversePrimer() {
 197                 return reversePrimer;
 198         }
 199         /**
 200          * @see #getReversePrimer()
 201          * @see #getForwardPrimer()
 202          */
 203         public void setReversePrimer(Primer reversePrimer) {
 204                 this.reversePrimer = reversePrimer;
 205         }
 206
 207
 208         /**
 209          * The material and/or method used for purification.
 210          */
 211         public MaterialOrMethodEvent getPurification() {
 212                 return purification;
 213         }
 214         /**
 215          * @see #getPurification()
 216          */
 217         public void setPurification(MaterialOrMethodEvent purification) {
 218                 this.purification = purification;
 219         }
 220
 221     /**
 222      * The institution in which the amplification event took place.
 223      * Usually the {@link Amplification#getActor()} should be a person
 224      * or team that works for this institution at the given time
 225      * @return the institution
 226      */
 227 //      #4498
 228     public Institution getInstitution() {
 229                 return institution;
 230         }
 231         /**
 232          * @see #getInstitution()
 233          */
 234         public void setInstitution(Institution institution) {
 235                 this.institution = institution;
 236         }
 237
 238         /**
 239          * The voltage used for running the electrophoresis quality check.
 240          * Base unit is voltage [V].
 241          * @see #getGelRunningTime()
 242          * @see #getGelPhoto()
 243          * @see #getLadderUsed()
 244          * @see #getGelConcentration()
 245
 246          */
 247         public Double getElectrophoresisVoltage() {
 248                 return electrophoresisVoltage;
 249         }
 250         /**
 251          * @see #getElectrophoresisVoltage()
 252          */
 253         public void setElectrophoresisVoltage(Double electrophoresisVoltage) {
 254                 this.electrophoresisVoltage = electrophoresisVoltage;
 255         }
 256
 257         /**
 258          * The time for running the electrophoresis quality check.
 259          * Base unit is minutes [min].
 260          */
 261         public Double getGelRunningTime() {
 262                 return gelRunningTime;
 263         }
 264         /**
 265          * @see #getGelRunningTime()
 266          */
 267         public void setGelRunningTime(Double gelRunningTime) {
 268                 this.gelRunningTime = gelRunningTime;
 269         }
 270
 271
 272         /**
 273          * The gel concentration used for the electrophoresis.
 274          * Base unit is [%]
 275          * @see #getElectrophoresisVoltage()
 276          * @see #getGelRunningTime()
 277          * @see #getGelPhoto()
 278          * @see #getLadderUsed()
 279          */
 280         public Double getGelConcentration() {
 281                 return gelConcentration;
 282         }
 283         /**
 284          * @see #getGelConcentration()
 285          */
 286         public void setGelConcentration(Double gelConcentration) {
 287                 this.gelConcentration = gelConcentration;
 288         }
 289
 290         /**
 291          * Material and method used for testing quality of this amplification.
 292          * @see #getElectrophoresisVoltage()
 293          * @see #getGelPhoto()
 294          * @see #getGelConcentration()
 295          * @see #getGelRunningTime()
 296          */
 297         public String getLadderUsed() {
 298                 return ladderUsed;
 299         }
 300         /**
 301          * @see #getLadderUsed()
 302          */
 303         public void setLadderUsed(String ladderUsed) {
 304                 this.ladderUsed = ladderUsed;
 305         }
 306
 307
 308         // ********************** CLONE ***********************************/
 309         /**
 310          * Clones <i>this</i> amplification. This is a shortcut that enables to create
 311          * a new instance that differs only slightly from <i>this</i> amplification by
 312          * modifying only some of the attributes.<BR><BR>
 313          *
 314          *
 315          * @see EventBase#clone()
 316          * @see java.lang.Object#clone()
 317          */
 318         @Override
 319         public Object clone()  {
 320                 try{
 321                         Amplification result = (Amplification)super.clone();
 322
 323                         //don't change marker, forwardPrimer, reversePrimer,
 324                         //purifiaction, ladderUsed, electrophoresisVoltage,
 325                         //gelRunningTime, gelConcentration
 326                         return result;
 327                 }catch (CloneNotSupportedException e) {
 328                         logger.warn("Object does not implement cloneable");
 329                         e.printStackTrace();
 330                         return null;
 331                 }
 332         }
 333
 334
 335 }