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