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 eu.etaxonomy.cdm.model.media.IMediaDocumented;
  14 import eu.etaxonomy.cdm.model.media.Media;
  15 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  16 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  17 import eu.etaxonomy.cdm.model.common.IReferencedEntity;
  18 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  19 import eu.etaxonomy.cdm.strategy.cache.common.IdentifiableEntityDefaultCacheStrategy;
  20
  21 import org.apache.log4j.Logger;
  22 import org.hibernate.annotations.Cascade;
  23 import org.hibernate.annotations.CascadeType;
  24 import org.hibernate.annotations.Index;
  25 import org.hibernate.annotations.Table;
  26 import org.hibernate.envers.Audited;
  27 import org.springframework.beans.factory.annotation.Configurable;
  28
  29 import java.util.*;
  30
  31 import javax.persistence.*;
  32 import javax.xml.bind.annotation.XmlAccessType;
  33 import javax.xml.bind.annotation.XmlAccessorType;
  34 import javax.xml.bind.annotation.XmlAttribute;
  35 import javax.xml.bind.annotation.XmlElement;
  36 import javax.xml.bind.annotation.XmlElementWrapper;
  37 import javax.xml.bind.annotation.XmlIDREF;
  38 import javax.xml.bind.annotation.XmlRootElement;
  39 import javax.xml.bind.annotation.XmlSchemaType;
  40 import javax.xml.bind.annotation.XmlType;
  41
  42 /**
  43  * @author m.doering
  44  * @version 1.0
  45  * @created 08-Nov-2007 13:06:51
  46  */
  47 @XmlAccessorType(XmlAccessType.FIELD)
  48 @XmlType(name = "Sequence", propOrder = {
  49     "sequence",
  50     "length",
  51     "dateSequenced",
  52     "barcode",
  53     "citationMicroReference",
  54     "publishedIn",
  55     "locus",
  56     "citations",
  57     "genBankAccession",
  58     "chromatograms"
  59 })
  60 @XmlRootElement(name = "Sequence")
  61 @Entity
  62 @Audited
  63 @Configurable
  64 @Table(appliesTo="Sequence", indexes = { @Index(name = "sequenceTitleCacheIndex", columnNames = { "titleCache" }) })
  65 public class Sequence extends IdentifiableEntity<IIdentifiableEntityCacheStrategy<Sequence>> implements IReferencedEntity, IMediaDocumented{
  66         private static final long serialVersionUID = 8298983152731241775L;
  67         private static final Logger logger = Logger.getLogger(Sequence.class);
  68
  69         //the sequence as a string of base pairs. 5'->3'
  70         @XmlElement(name = "Sequence")
  71         private String sequence;
  72
  73         //should be calculated in case sequence is set
  74         @XmlElement(name = "Length")
  75         private Integer length;
  76
  77         //should be calculated in case sequence is set
  78         @XmlElement(name = "DateSequenced")
  79         @Temporal(TemporalType.DATE)
  80         private Calendar dateSequenced;
  81
  82         //should be calculated in case sequence is set
  83         @XmlAttribute(name = "isBarcode")
  84         private boolean barcode;
  85
  86         //the sequence as a string of base pairs. 5'->3'
  87         @XmlElement(name = "CitationMicroReference")
  88         private String citationMicroReference;
  89
  90         @XmlElement(name = "PublishedIn")
  91     @XmlIDREF
  92     @XmlSchemaType(name = "IDREF")
  93     @ManyToOne(fetch = FetchType.LAZY)
  94     @Cascade(CascadeType.SAVE_UPDATE)
  95         private ReferenceBase publishedIn;
  96
  97         @XmlElementWrapper(name = "Citations")
  98         @XmlElement(name = "Citation")
  99     @XmlIDREF
 100     @XmlSchemaType(name = "IDREF")
 101     @OneToMany(fetch = FetchType.LAZY)
 102         private Set<ReferenceBase> citations = new HashSet<ReferenceBase>();
 103
 104         @XmlElementWrapper(name = "GenBankAccessions")
 105         @XmlElement(name = "GenBankAccession")
 106     @OneToMany(fetch = FetchType.LAZY)
 107         private Set<GenBankAccession> genBankAccession = new HashSet<GenBankAccession>();
 108
 109         @XmlElement(name = "Locus")
 110     @XmlIDREF
 111     @XmlSchemaType(name = "IDREF")
 112     @ManyToOne(fetch = FetchType.LAZY)
 113     @Cascade(CascadeType.SAVE_UPDATE)
 114         private Locus locus;
 115
 116         @XmlElementWrapper(name = "Chromatograms")
 117         @XmlElement(name = "Chromatogram")
 118     @XmlIDREF
 119     @XmlSchemaType(name = "IDREF")
 120     @OneToMany(fetch = FetchType.LAZY)
 121         private Set<Media> chromatograms = new HashSet<Media>();
 122
 123         protected Sequence() {
 124                 super(); // FIXME I think this is explicit - do we really need to call this?
 125                 this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Sequence>();
 126         }
 127
 128         public Locus getLocus(){
 129                 logger.debug("getLocus");
 130                 return this.locus;
 131         }
 132
 133         public void setLocus(Locus locus){
 134                 this.locus = locus;
 135         }
 136
 137         public ReferenceBase getPublishedIn(){
 138                 return this.publishedIn;
 139         }
 140
 141         public void setPublishedIn(ReferenceBase publishedIn){
 142                 this.publishedIn = publishedIn;
 143         }
 144
 145         public Set<ReferenceBase> getCitations() {
 146                 return citations;
 147         }
 148         protected void setCitations(Set<ReferenceBase> citations) {
 149                 this.citations = citations;
 150         }
 151         public void addCitation(ReferenceBase citation) {
 152                 this.citations.add(citation);
 153         }
 154         public void removeCitation(ReferenceBase citation) {
 155                 this.citations.remove(citation);
 156         }
 157
 158         public Set<GenBankAccession> getGenBankAccession() {
 159                 return genBankAccession;
 160         }
 161
 162         public void addGenBankAccession(GenBankAccession genBankAccession) {
 163                 this.genBankAccession.add(genBankAccession);
 164         }
 165
 166         public void removeGenBankAccession(GenBankAccession genBankAccession) {
 167                 this.genBankAccession.remove(genBankAccession);
 168         }
 169
 170         public Set<Media> getChromatograms() {
 171                 return chromatograms;
 172         }
 173
 174         public void addChromatogram(Media chromatogram) {
 175                 this.chromatograms.add(chromatogram);
 176         }
 177
 178         public void removeChromatogram(Media chromatogram) {
 179                 this.chromatograms.remove(chromatogram);
 180         }
 181
 182         @Transient
 183         public Set<Media> getMedia() {
 184                 return getChromatograms();
 185         }
 186
 187         public String getSequence(){
 188                 return this.sequence;
 189         }
 190
 191         /**
 192          *
 193          * @param sequence    sequence
 194          */
 195         public void setSequence(String sequence){
 196                 this.sequence = sequence;
 197         }
 198
 199         public Integer getLength(){
 200                 return this.length;
 201         }
 202
 203         /**
 204          *
 205          * @param length    length
 206          */
 207         public void setLength(Integer length){
 208                 this.length = length;
 209         }
 210
 211         public Calendar getDateSequenced(){
 212                 return this.dateSequenced;
 213         }
 214
 215         /**
 216          *
 217          * @param dateSequenced    dateSequenced
 218          */
 219         public void setDateSequenced(Calendar dateSequenced){
 220                 this.dateSequenced = dateSequenced;
 221         }
 222
 223         public boolean isBarcode(){
 224                 return this.barcode;
 225         }
 226
 227         /**
 228          *
 229          * @param isBarcode    isBarcode
 230          */
 231         public void setBarcode(boolean barcode){
 232                 this.barcode = barcode;
 233         }
 234
 235         public String getCitationMicroReference(){
 236                 return this.citationMicroReference;
 237         }
 238
 239         /**
 240          *
 241          * @param citationMicroReference    citationMicroReference
 242          */
 243         public void setCitationMicroReference(String citationMicroReference){
 244                 this.citationMicroReference = citationMicroReference;
 245         }
 246
 247         public ReferenceBase getCitation(){
 248                 return publishedIn;
 249         }
 250 }