cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/SingleRead.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.ManyToOne;
  14 import javax.persistence.Transient;
  15 import javax.xml.bind.annotation.XmlAccessType;
  16 import javax.xml.bind.annotation.XmlAccessorType;
  17 import javax.xml.bind.annotation.XmlAttribute;
  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.Type;
  26 import org.hibernate.envers.Audited;
  27
  28 import eu.etaxonomy.cdm.model.agent.AgentBase;
  29 import eu.etaxonomy.cdm.model.common.EventBase;
  30 import eu.etaxonomy.cdm.model.common.TimePeriod;
  31 import eu.etaxonomy.cdm.model.media.Media;
  32 import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
  33
  34 /**
  35  * Instances of this the {@link SingleRead} class describe the process and the result of a single
  36  * sequence generation (read). It has as an input the PCR result ({@link Amplification}). A primer
  37  * is used for expressing the DNA in either {@link SequenceDirection#Forward forward} or
  38  * {@link SequenceDirection#Reverse reverse} direction.
  39  * The result of the process is a {@link #getPherogram() pherogram} which by interpretation results
  40  * in the most probable {@link #getSequence() sequence}.
  41  * The event dates like the sequencing date and the sequencing agent(person) are inherited by {@link EventBase}.
  42  *
  43  * @see Amplification
  44  * @see SequenceString
  45  * @see Sequence
  46  *
  47  * @author a.mueller
  48  * @created 2013-07-05
  49  */
  50 @XmlAccessorType(XmlAccessType.FIELD)
  51 @XmlType(name = "SingleRead", propOrder = {
  52         "amplification",
  53         "sequence",
  54         "primer",
  55         "direction",
  56         "pherogram",
  57         "materialOrMethod"
  58 })
  59 @XmlRootElement(name = "Primer")
  60 @Entity
  61 @Audited
  62 public class SingleRead extends EventBase implements Cloneable{
  63         private static final long serialVersionUID = 1735535003073536132L;
  64         private static final Logger logger = Logger.getLogger(SingleRead.class);
  65
  66         /** @see #getAmplification()  */
  67         @XmlElement(name = "Amplification")
  68     @XmlIDREF
  69     @XmlSchemaType(name = "IDREF")
  70     @ManyToOne(fetch = FetchType.LAZY)
  71         private Amplification amplification;
  72
  73         /** @see #getPrimer()*/
  74         @XmlElement(name = "Primer")
  75     @XmlIDREF
  76     @XmlSchemaType(name = "IDREF")
  77     @ManyToOne(fetch = FetchType.LAZY)
  78         private Primer primer;
  79
  80         /** @see #getSequence()*/
  81         /**{@link #getSequence()}*/
  82         @XmlElement(name = "Sequence")
  83     private SequenceString sequence = SequenceString.NewInstance();
  84
  85         @XmlElement(name = "Pherogram")
  86     @XmlIDREF
  87     @XmlSchemaType(name = "IDREF")
  88     @ManyToOne(fetch = FetchType.LAZY)
  89         private Media pherogram;
  90
  91         /** @see #getDirection()*/
  92         @XmlAttribute(name ="direction")
  93         //TODO length = 3
  94         @Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",
  95         parameters = {@org.hibernate.annotations.Parameter(name  = "enumClass", value = "eu.etaxonomy.cdm.model.molecular.SequenceDirection")}
  96         )
  97         private SequenceDirection direction;
  98
  99         @XmlElement(name = "MaterialOrMethod")
 100     @XmlIDREF
 101     @XmlSchemaType(name = "IDREF")
 102     @ManyToOne(fetch = FetchType.LAZY)
 103         private MaterialOrMethodEvent materialOrMethod;
 104
 105
 106         // ******************** FACTORY METHOD ******************/
 107
 108         public static SingleRead NewInstance(){
 109                 return new SingleRead();
 110         }
 111
 112         // ********************* CONSTRUCTOR ********************/
 113
 114         private SingleRead(){};
 115
 116         // ********************* GETTER / SETTER ********************/
 117
 118
 119         /**
 120          * Returns the {@link Amplification amplification} that was the input for this
 121          * {@link SingleRead single sequence}.
 122          */
 123         public Amplification getAmplification() {
 124                 return amplification;
 125         }
 126
 127         /**
 128          * TODO this method is protected as long as bidirectionality is not clear.
 129          * @see #getAmplification()
 130          */
 131         protected void setAmplification(Amplification amplification) {
 132                 this.amplification = amplification;
 133         }
 134
 135         /**
 136          * The {@link Primer primer} used for processing this single sequence.
 137          * Often this primer already has been used in the according amplification.
 138          * However, there are exceptions from this rule.
 139          */
 140         public Primer getPrimer() {
 141                 return primer;
 142         }
 143
 144         /**
 145          * @see #getPrimer()
 146          */
 147         public void setPrimer(Primer primer) {
 148                 this.primer = primer;
 149         }
 150
 151         /**
 152          * The {@link SequenceString sequence string} of this single sequence process (e.g. AGTGGTAGGATG)
 153          */
 154         public SequenceString getSequence() {
 155                 return sequence;
 156         }
 157
 158         /**
 159          * @see #getSequence()
 160          */
 161         public void setSequence(SequenceString sequence) {
 162                 if (sequence == null){
 163                         SequenceString.NewInstance();
 164                 }
 165                 this.sequence = sequence;
 166         }
 167
 168         /**
 169          * The {@link SequenceDirection direction} in which this single sequence has been created.
 170          * Usually an {@link Amplification amplification} leads to 2 single sequences a
 171          * {@link SequenceDirection#Forward forward} and a {@link SequenceDirection#Reverse reverse} one.
 172          * These 2 result then in a {@link Sequence consensus sequence}.
 173          * But there are exceptions from this rule.
 174          */
 175         public SequenceDirection getDirection() {
 176                 return direction;
 177         }
 178
 179         /**
 180          * @see #getDirection()
 181          */
 182         public void setDirection(SequenceDirection direction) {
 183                 this.direction = direction;
 184         }
 185
 186         /**
 187          * The pherogram (chromatogram) which visualizes the result of this single sequence.
 188          */
 189         public Media getPherogram() {
 190                 return pherogram;
 191         }
 192
 193         /**
 194          * @see #getPherogram()
 195          */
 196         public void setPherogram(Media pherogram) {
 197                 this.pherogram = pherogram;
 198         }
 199
 200
 201         /**
 202          * The material and/or method used for this sequencing.
 203          */
 204         public MaterialOrMethodEvent getMaterialOrMethod() {
 205                 return materialOrMethod;
 206         }
 207
 208         /**
 209          * @see #getMaterialOrMethod()
 210          */
 211         public void setMaterialOrMethod(MaterialOrMethodEvent materialOrMethod) {
 212                 this.materialOrMethod = materialOrMethod;
 213         }
 214
 215
 216
 217 //*************************** Transient GETTER /SETTER *****************************/
 218         /**
 219          * Delegate method to get the text representation of the {@link #getSequence() sequence}.
 220          * @see #setSequenceString(String)
 221          */
 222         @Transient
 223         public String getSequenceString() {
 224                 return sequence.getString();
 225         }
 226
 227         /**
 228          * Delegate method to set the text representation of the {@link #getSequence() sequence}.
 229          */
 230         @Transient
 231         public void setSequenceString(String sequence) {
 232                 this.sequence.setString(sequence);
 233         }
 234
 235         /**
 236          * Transient convenience method which wrapps {@link EventBase#getActor()}.
 237          * @return the {@link TimePeriod date/period} when this sequence was created.
 238          */
 239         @Transient
 240         public TimePeriod getDateSequenced(){
 241                 return ((EventBase)this).getTimeperiod();
 242         }
 243
 244         /**
 245          * @see #getDateSequenced()
 246          */
 247         public void setDateSequenced(TimePeriod dateSequenced){
 248                 this.setTimeperiod(dateSequenced);
 249         }
 250
 251         /**
 252          * Transient convenience method which wrapps {@link EventBase#getActor()}.
 253          * @return the {@link AgentBase agent} who sequenced this single sequence.
 254          */
 255         @Transient
 256         public AgentBase getSequencedBy(){
 257                 return ((EventBase)this).getActor();
 258         }
 259
 260         /**
 261          * @see #getSequencedBy()
 262          */
 263         public void setSequencedBy(AgentBase sequencedBy){
 264                 this.setActor(sequencedBy);
 265         }
 266
 267
 268         // ********************* CLONE ********************/
 269         /**
 270          * Clones <i>this</i> sequence. This is a shortcut that enables to create
 271          * a new instance that differs only slightly from <i>this</i> sequencing by
 272          * modifying only some of the attributes.<BR><BR>
 273          *
 274          *
 275          * @see eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
 276          * @see java.lang.Object#clone()
 277          */
 278         @Override
 279         public Object clone()  {
 280                 try{
 281                 SingleRead result = (SingleRead)super.clone();
 282
 283                 //sequences
 284                 result.sequence = (SequenceString)this.sequence.clone();
 285
 286
 287                 //Don't change amplification, pherogram, primer, sequence, direction
 288                 return result;
 289
 290                 }catch (CloneNotSupportedException e) {
 291                         logger.warn("Object does not implement cloneable");
 292                         e.printStackTrace();
 293                         return null;
 294                 }
 295         }
 296
 297 }