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.hibernate.search.annotations.Field;
  28 import org.hibernate.search.annotations.Indexed;
  29 import org.springframework.beans.factory.annotation.Configurable;
  30
  31 import java.util.*;
  32
  33 import javax.persistence.*;
  34 import javax.xml.bind.annotation.XmlAccessType;
  35 import javax.xml.bind.annotation.XmlAccessorType;
  36 import javax.xml.bind.annotation.XmlAttribute;
  37 import javax.xml.bind.annotation.XmlElement;
  38 import javax.xml.bind.annotation.XmlElementWrapper;
  39 import javax.xml.bind.annotation.XmlIDREF;
  40 import javax.xml.bind.annotation.XmlRootElement;
  41 import javax.xml.bind.annotation.XmlSchemaType;
  42 import javax.xml.bind.annotation.XmlType;
  43
  44 /**
  45  * @author m.doering
  46  * @version 1.0
  47  * @created 08-Nov-2007 13:06:51
  48  */
  49 @XmlAccessorType(XmlAccessType.FIELD)
  50 @XmlType(name = "Sequence", propOrder = {
  51     "sequence",
  52     "length",
  53     "dateSequenced",
  54     "barcode",
  55     "citationMicroReference",
  56     "publishedIn",
  57     "locus",
  58     "citations",
  59     "genBankAccession",
  60     "chromatograms"
  61 })
  62 @XmlRootElement(name = "Sequence")
  63 @Entity
  64 @Audited
  65 @Configurable
  66 @Table(appliesTo="Sequence", indexes = { @Index(name = "sequenceTitleCacheIndex", columnNames = { "titleCache" }) })
  67 public class Sequence extends IdentifiableEntity<IIdentifiableEntityCacheStrategy<Sequence>> implements IReferencedEntity, IMediaDocumented{
  68         private static final long serialVersionUID = 8298983152731241775L;
  69         private static final Logger logger = Logger.getLogger(Sequence.class);
  70
  71         //the sequence as a string of base pairs. 5'->3'
  72         @XmlElement(name = "Sequence")
  73         private String sequence;
  74
  75         //should be calculated in case sequence is set
  76         @XmlElement(name = "Length")
  77         private Integer length;
  78
  79         //should be calculated in case sequence is set
  80         // FIXME Should be a DateTime
  81         @XmlElement(name = "DateSequenced")
  82         @Temporal(TemporalType.DATE)
  83         private Calendar dateSequenced;
  84
  85         //should be calculated in case sequence is set
  86         @XmlAttribute(name = "isBarcode")
  87         private boolean barcode;
  88
  89         //the sequence as a string of base pairs. 5'->3'
  90         @XmlElement(name = "CitationMicroReference")
  91         private String citationMicroReference;
  92
  93         @XmlElement(name = "PublishedIn")
  94     @XmlIDREF
  95     @XmlSchemaType(name = "IDREF")
  96     @ManyToOne(fetch = FetchType.LAZY)
  97     @Cascade(CascadeType.SAVE_UPDATE)
  98         private ReferenceBase publishedIn;
  99
 100         @XmlElementWrapper(name = "Citations")
 101         @XmlElement(name = "Citation")
 102     @XmlIDREF
 103     @XmlSchemaType(name = "IDREF")
 104     @OneToMany(fetch = FetchType.LAZY)
 105         private Set<ReferenceBase> citations = new HashSet<ReferenceBase>();
 106
 107         @XmlElementWrapper(name = "GenBankAccessions")
 108         @XmlElement(name = "GenBankAccession")
 109     @OneToMany(fetch = FetchType.LAZY)
 110         private Set<GenBankAccession> genBankAccession = new HashSet<GenBankAccession>();
 111
 112         @XmlElement(name = "Locus")
 113     @XmlIDREF
 114     @XmlSchemaType(name = "IDREF")
 115     @ManyToOne(fetch = FetchType.LAZY)
 116     @Cascade(CascadeType.SAVE_UPDATE)
 117         private Locus locus;
 118
 119         @XmlElementWrapper(name = "Chromatograms")
 120         @XmlElement(name = "Chromatogram")
 121     @XmlIDREF
 122     @XmlSchemaType(name = "IDREF")
 123     @OneToMany(fetch = FetchType.LAZY)
 124         private Set<Media> chromatograms = new HashSet<Media>();
 125
 126         protected Sequence() {
 127                 super(); // FIXME I think this is explicit - do we really need to call this?
 128                 this.cacheStrategy = new IdentifiableEntityDefaultCacheStrategy<Sequence>();
 129         }
 130
 131         public Locus getLocus(){
 132                 logger.debug("getLocus");
 133                 return this.locus;
 134         }
 135
 136         public void setLocus(Locus locus){
 137                 this.locus = locus;
 138         }
 139
 140         public ReferenceBase getPublishedIn(){
 141                 return this.publishedIn;
 142         }
 143
 144         public void setPublishedIn(ReferenceBase publishedIn){
 145                 this.publishedIn = publishedIn;
 146         }
 147
 148         public Set<ReferenceBase> getCitations() {
 149                 return citations;
 150         }
 151         protected void setCitations(Set<ReferenceBase> citations) {
 152                 this.citations = citations;
 153         }
 154         public void addCitation(ReferenceBase citation) {
 155                 this.citations.add(citation);
 156         }
 157         public void removeCitation(ReferenceBase citation) {
 158                 this.citations.remove(citation);
 159         }
 160
 161         public Set<GenBankAccession> getGenBankAccession() {
 162                 return genBankAccession;
 163         }
 164
 165         public void addGenBankAccession(GenBankAccession genBankAccession) {
 166                 this.genBankAccession.add(genBankAccession);
 167         }
 168
 169         public void removeGenBankAccession(GenBankAccession genBankAccession) {
 170                 this.genBankAccession.remove(genBankAccession);
 171         }
 172
 173         public Set<Media> getChromatograms() {
 174                 return chromatograms;
 175         }
 176
 177         public void addChromatogram(Media chromatogram) {
 178                 this.chromatograms.add(chromatogram);
 179         }
 180
 181         public void removeChromatogram(Media chromatogram) {
 182                 this.chromatograms.remove(chromatogram);
 183         }
 184
 185         @Transient
 186         public Set<Media> getMedia() {
 187                 return getChromatograms();
 188         }
 189
 190         public String getSequence(){
 191                 return this.sequence;
 192         }
 193
 194         /**
 195          *
 196          * @param sequence    sequence
 197          */
 198         public void setSequence(String sequence){
 199                 this.sequence = sequence;
 200         }
 201
 202         public Integer getLength(){
 203                 return this.length;
 204         }
 205
 206         /**
 207          *
 208          * @param length    length
 209          */
 210         public void setLength(Integer length){
 211                 this.length = length;
 212         }
 213
 214         public Calendar getDateSequenced(){
 215                 return this.dateSequenced;
 216         }
 217
 218         /**
 219          *
 220          * @param dateSequenced    dateSequenced
 221          */
 222         public void setDateSequenced(Calendar dateSequenced){
 223                 this.dateSequenced = dateSequenced;
 224         }
 225
 226         public boolean isBarcode(){
 227                 return this.barcode;
 228         }
 229
 230         /**
 231          *
 232          * @param isBarcode    isBarcode
 233          */
 234         public void setBarcode(boolean barcode){
 235                 this.barcode = barcode;
 236         }
 237
 238         public String getCitationMicroReference(){
 239                 return this.citationMicroReference;
 240         }
 241
 242         /**
 243          *
 244          * @param citationMicroReference    citationMicroReference
 245          */
 246         public void setCitationMicroReference(String citationMicroReference){
 247                 this.citationMicroReference = citationMicroReference;
 248         }
 249
 250         public ReferenceBase getCitation(){
 251                 return publishedIn;
 252         }
 253 }