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 org.apache.log4j.Logger;
  19 import org.hibernate.annotations.Index;
  20 import org.hibernate.annotations.Table;
  21
  22 import java.util.*;
  23
  24 import javax.persistence.*;
  25
  26 /**
  27  * @author m.doering
  28  * @version 1.0
  29  * @created 08-Nov-2007 13:06:51
  30  */
  31 @Entity
  32 @Table(appliesTo="Sequence", indexes = { @Index(name = "sequenceTitleCacheIndex", columnNames = { "persistentTitleCache" }) })
  33 public class Sequence extends IdentifiableEntity implements IReferencedEntity, IMediaDocumented{
  34         private static final Logger logger = Logger.getLogger(Sequence.class);
  35
  36         //the sequence as a string of base pairs. 5'->3'
  37         private String sequence;
  38         //should be calculated in case sequence is set
  39         private Integer length;
  40         //should be calculated in case sequence is set
  41         private Calendar dateSequenced;
  42         //should be calculated in case sequence is set
  43         private boolean isBarcode;
  44         //the sequence as a string of base pairs. 5'->3'
  45         private String citationMicroReference;
  46         private ReferenceBase publishedIn;
  47         private Set<ReferenceBase> citations = new HashSet();
  48         private Set<GenBankAccession> genBankAccession = new HashSet();
  49         private Locus locus;
  50         private Set<Media> chromatograms = new HashSet();
  51
  52         @ManyToOne
  53         public Locus getLocus(){
  54                 return this.locus;
  55         }
  56         public void setLocus(Locus locus){
  57                 this.locus = locus;
  58         }
  59
  60         @ManyToOne
  61         public ReferenceBase getPublishedIn(){
  62                 return this.publishedIn;
  63         }
  64         public void setPublishedIn(ReferenceBase publishedIn){
  65                 this.publishedIn = publishedIn;
  66         }
  67
  68
  69
  70         @OneToMany
  71         public Set<ReferenceBase> getCitations() {
  72                 return citations;
  73         }
  74         protected void setCitations(Set<ReferenceBase> citations) {
  75                 this.citations = citations;
  76         }
  77         public void addCitation(ReferenceBase citation) {
  78                 this.citations.add(citation);
  79         }
  80         public void removeCitation(ReferenceBase citation) {
  81                 this.citations.remove(citation);
  82         }
  83
  84
  85         @OneToMany
  86         public Set<GenBankAccession> getGenBankAccession() {
  87                 return genBankAccession;
  88         }
  89
  90         protected void setGenBankAccession(Set<GenBankAccession> genBankAccession) {
  91                 this.genBankAccession = genBankAccession;
  92         }
  93         public void addGenBankAccession(GenBankAccession genBankAccession) {
  94                 this.genBankAccession.add(genBankAccession);
  95         }
  96         public void removeGenBankAccession(GenBankAccession genBankAccession) {
  97                 this.genBankAccession.remove(genBankAccession);
  98         }
  99
 100
 101         @OneToMany
 102         public Set<Media> getChromatograms() {
 103                 return chromatograms;
 104         }
 105
 106         protected void setChromatograms(Set<Media> chromatograms) {
 107                 this.chromatograms = chromatograms;
 108         }
 109         public void addChromatogram(Media chromatogram) {
 110                 this.chromatograms.add(chromatogram);
 111         }
 112         public void removeChromatogram(Media chromatogram) {
 113                 this.chromatograms.remove(chromatogram);
 114         }
 115
 116         @Transient
 117         public Set<Media> getMedia() {
 118                 return getChromatograms();
 119         }
 120
 121
 122         public String getSequence(){
 123                 return this.sequence;
 124         }
 125
 126         /**
 127          *
 128          * @param sequence    sequence
 129          */
 130         public void setSequence(String sequence){
 131                 this.sequence = sequence;
 132         }
 133
 134         public Integer getLength(){
 135                 return this.length;
 136         }
 137
 138         /**
 139          *
 140          * @param length    length
 141          */
 142         public void setLength(Integer length){
 143                 this.length = length;
 144         }
 145
 146         @Temporal(TemporalType.DATE)
 147         public Calendar getDateSequenced(){
 148                 return this.dateSequenced;
 149         }
 150
 151         /**
 152          *
 153          * @param dateSequenced    dateSequenced
 154          */
 155         public void setDateSequenced(Calendar dateSequenced){
 156                 this.dateSequenced = dateSequenced;
 157         }
 158
 159         public boolean isBarcode(){
 160                 return this.isBarcode;
 161         }
 162
 163         /**
 164          *
 165          * @param isBarcode    isBarcode
 166          */
 167         public void setBarcode(boolean isBarcode){
 168                 this.isBarcode = isBarcode;
 169         }
 170
 171         public String getCitationMicroReference(){
 172                 return this.citationMicroReference;
 173         }
 174
 175         /**
 176          *
 177          * @param citationMicroReference    citationMicroReference
 178          */
 179         public void setCitationMicroReference(String citationMicroReference){
 180                 this.citationMicroReference = citationMicroReference;
 181         }
 182
 183         public String generateTitle(){
 184                 return "";
 185         }
 186
 187         @Transient
 188         public ReferenceBase getCitation(){
 189                 return null;
 190         }
 191
 192 }