cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/Sequence.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
  10 package eu.etaxonomy.cdm.model.molecular;
  11
  12
  13 import java.util.HashSet;
  14 import java.util.Set;
  15
  16 import javax.persistence.Basic;
  17 import javax.persistence.Entity;
  18 import javax.persistence.FetchType;
  19 import javax.persistence.Lob;
  20 import javax.persistence.ManyToOne;
  21 import javax.persistence.OneToMany;
  22 import javax.persistence.Transient;
  23 import javax.xml.bind.annotation.XmlAccessType;
  24 import javax.xml.bind.annotation.XmlAccessorType;
  25 import javax.xml.bind.annotation.XmlAttribute;
  26 import javax.xml.bind.annotation.XmlElement;
  27 import javax.xml.bind.annotation.XmlElementWrapper;
  28 import javax.xml.bind.annotation.XmlIDREF;
  29 import javax.xml.bind.annotation.XmlRootElement;
  30 import javax.xml.bind.annotation.XmlSchemaType;
  31 import javax.xml.bind.annotation.XmlType;
  32 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
  33
  34 import org.apache.log4j.Logger;
  35 import org.hibernate.annotations.Cascade;
  36 import org.hibernate.annotations.CascadeType;
  37 import org.hibernate.annotations.Index;
  38 import org.hibernate.annotations.Table;
  39 import org.hibernate.annotations.Type;
  40 import org.hibernate.envers.Audited;
  41 import org.joda.time.DateTime;
  42 import org.springframework.beans.factory.annotation.Configurable;
  43
  44 import eu.etaxonomy.cdm.jaxb.DateTimeAdapter;
  45 import eu.etaxonomy.cdm.model.common.IReferencedEntity;
  46 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  47 import eu.etaxonomy.cdm.model.media.IMediaDocumented;
  48 import eu.etaxonomy.cdm.model.media.Media;
  49 import eu.etaxonomy.cdm.model.reference.Reference;
  50 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  51 import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
  52
  53 /**
  54  * @author m.doering
  55  * @version 1.0
  56  * @created 08-Nov-2007 13:06:51
  57  */
  58 @XmlAccessorType(XmlAccessType.FIELD)
  59 @XmlType(name = "Sequence", propOrder = {
  60     "sequence",
  61     "length",
  62     "dateSequenced",
  63     "barcode",
  64     "citationMicroReference",
  65     "publishedIn",
  66     "locus",
  67     "citations",
  68     "genBankAccession",
  69     "chromatograms"
  70 })
  71 @XmlRootElement(name = "Sequence")
  72 @Entity
  73 @Audited
  74 @Configurable
  75 @Table(appliesTo="Sequence", indexes = { @Index(name = "sequenceTitleCacheIndex", columnNames = { "titleCache" }) })
  76 public class Sequence extends IdentifiableEntity<IIdentifiableEntityCacheStrategy<Sequence>> implements IReferencedEntity, IMediaDocumented{
  77         private static final long serialVersionUID = 8298983152731241775L;
  78         private static final Logger logger = Logger.getLogger(Sequence.class);
  79
  80         //the sequence as a string of base pairs. 5'->3'
  81         @XmlElement(name = "Sequence")
  82     @Lob
  83         private String sequence;
  84
  85         //should be calculated in case sequence is set
  86         @XmlElement(name = "Length")
  87         private Integer length;
  88
  89         //should be calculated in case sequence is set
  90         @XmlElement (name = "DateSequenced", type= String.class)
  91         @XmlJavaTypeAdapter(DateTimeAdapter.class)
  92         @Type(type="dateTimeUserType")
  93         @Basic(fetch = FetchType.LAZY)
  94         private DateTime dateSequenced;
  95
  96         //should be calculated in case sequence is set
  97         @XmlAttribute(name = "isBarcode")
  98         private boolean barcode;
  99
 100         //the sequence as a string of base pairs. 5'->3'
 101         @XmlElement(name = "CitationMicroReference")
 102         private String citationMicroReference;
 103
 104         @XmlElement(name = "PublishedIn")
 105     @XmlIDREF
 106     @XmlSchemaType(name = "IDREF")
 107     @ManyToOne(fetch = FetchType.LAZY)
 108     @Cascade(CascadeType.SAVE_UPDATE)
 109         private Reference<?> publishedIn;
 110
 111         @XmlElementWrapper(name = "Citations")
 112         @XmlElement(name = "Citation")
 113     @XmlIDREF
 114     @XmlSchemaType(name = "IDREF")
 115     @OneToMany(fetch = FetchType.LAZY)
 116         private Set<Reference> citations = new HashSet<Reference>();
 117
 118         @XmlElementWrapper(name = "GenBankAccessions")
 119         @XmlElement(name = "GenBankAccession")
 120     @OneToMany(fetch = FetchType.LAZY)
 121         @Cascade(CascadeType.SAVE_UPDATE)
 122     private Set<GenBankAccession> genBankAccession = new HashSet<GenBankAccession>();
 123
 124         @XmlElement(name = "Locus")
 125     @XmlIDREF
 126     @XmlSchemaType(name = "IDREF")
 127     @ManyToOne(fetch = FetchType.LAZY)
 128     @Cascade(CascadeType.SAVE_UPDATE)
 129         private Locus locus;
 130
 131         @XmlElementWrapper(name = "Chromatograms")
 132         @XmlElement(name = "Chromatogram")
 133     @XmlIDREF
 134     @XmlSchemaType(name = "IDREF")
 135     @OneToMany(fetch = FetchType.LAZY)
 136         private Set<Media> chromatograms = new HashSet<Media>();
 137
 138 //*********************** FACTORY ****************************************************/
 139
 140         public static Sequence NewInstance(String sequence){
 141                 Sequence result = new Sequence();
 142                 result.setSequence(sequence);
 143                 return result;
 144         }
 145
 146 //*********************** CONSTRUCTOR ****************************************************/
 147
 148         protected Sequence() {
 149                 super(); // FIXME I think this is explicit - do we really need to call this?
 150                 this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Sequence>();
 151         }
 152
 153 //*********************** GETTER / SETTER ****************************************************/
 154
 155         public Locus getLocus(){
 156                 return this.locus;
 157         }
 158
 159         public void setLocus(Locus locus){
 160                 this.locus = locus;
 161         }
 162
 163         public Reference getPublishedIn(){
 164                 return this.publishedIn;
 165         }
 166
 167         public void setPublishedIn(Reference publishedIn){
 168                 this.publishedIn = publishedIn;
 169         }
 170
 171         public Set<Reference> getCitations() {
 172                 return citations;
 173         }
 174         protected void setCitations(Set<Reference> citations) {
 175                 this.citations = citations;
 176         }
 177         public void addCitation(Reference citation) {
 178                 this.citations.add(citation);
 179         }
 180         public void removeCitation(Reference citation) {
 181                 this.citations.remove(citation);
 182         }
 183
 184         public Set<GenBankAccession> getGenBankAccession() {
 185                 return genBankAccession;
 186         }
 187
 188         public void addGenBankAccession(GenBankAccession genBankAccession) {
 189                 this.genBankAccession.add(genBankAccession);
 190         }
 191
 192         public void removeGenBankAccession(GenBankAccession genBankAccession) {
 193                 this.genBankAccession.remove(genBankAccession);
 194         }
 195
 196         public Set<Media> getChromatograms() {
 197                 return chromatograms;
 198         }
 199
 200         public void addChromatogram(Media chromatogram) {
 201                 this.chromatograms.add(chromatogram);
 202         }
 203
 204         public void removeChromatogram(Media chromatogram) {
 205                 this.chromatograms.remove(chromatogram);
 206         }
 207
 208         @Transient
 209         public Set<Media> getMedia() {
 210                 return getChromatograms();
 211         }
 212
 213         public String getSequence(){
 214                 return this.sequence;
 215         }
 216
 217         /**
 218          *
 219          * @param sequence    sequence
 220          */
 221         public void setSequence(String sequence){
 222                 this.sequence = sequence;
 223         }
 224
 225         public Integer getLength(){
 226                 return this.length;
 227         }
 228
 229         /**
 230          *
 231          * @param length    length
 232          */
 233         public void setLength(Integer length){
 234                 this.length = length;
 235         }
 236
 237         public DateTime getDateSequenced(){
 238                 return this.dateSequenced;
 239         }
 240
 241         /**
 242          *
 243          * @param dateSequenced    dateSequenced
 244          */
 245         public void setDateSequenced(DateTime dateSequenced){
 246                 this.dateSequenced = dateSequenced;
 247         }
 248
 249         public boolean isBarcode(){
 250                 return this.barcode;
 251         }
 252
 253         /**
 254          *
 255          * @param isBarcode    isBarcode
 256          */
 257         public void setBarcode(boolean barcode){
 258                 this.barcode = barcode;
 259         }
 260
 261         public String getCitationMicroReference(){
 262                 return this.citationMicroReference;
 263         }
 264
 265         /**
 266          *
 267          * @param citationMicroReference    citationMicroReference
 268          */
 269         public void setCitationMicroReference(String citationMicroReference){
 270                 this.citationMicroReference = citationMicroReference;
 271         }
 272
 273         public Reference getCitation(){
 274                 return publishedIn;
 275         }
 276
 277         //*********************** CLONE ********************************************************/
 278         /**
 279          * Clones <i>this</i> sequence. This is a shortcut that enables to create
 280          * a new instance that differs only slightly from <i>this</i> sequence by
 281          * modifying only some of the attributes.<BR><BR>
 282          *
 283          *
 284          * @see eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
 285          * @see java.lang.Object#clone()
 286          */
 287         @Override
 288         public Object clone()  {
 289                 try{
 290                 Sequence result = (Sequence)super.clone();
 291
 292                 result.citations = new HashSet<Reference>();
 293                 for (Reference ref: this.citations){
 294                         result.citations.add((Reference) ref.clone());
 295
 296                 }
 297
 298                 result.genBankAccession = new HashSet<GenBankAccession>();
 299                 for (GenBankAccession genBankAcc: this.genBankAccession){
 300                         result.genBankAccession.add((GenBankAccession)genBankAcc.clone());
 301                 }
 302
 303                 result.chromatograms = new HashSet<Media>();
 304
 305                 for (Media chromatogram: this.chromatograms){
 306                         result.chromatograms.add((Media)chromatogram.clone());
 307                 }
 308
 309                 return result;
 310                 }catch (CloneNotSupportedException e) {
 311                         logger.warn("Object does not implement cloneable");
 312                         e.printStackTrace();
 313                         return null;
 314                 }
 315         }
 316 }