cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/molecular/PhylogeneticTree.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.ReferencedMedia;
  14
  15 import org.apache.log4j.Logger;
  16 import org.hibernate.envers.Audited;
  17 import org.hibernate.search.annotations.Indexed;
  18
  19 import java.util.*;
  20
  21 import javax.persistence.*;
  22 import javax.xml.bind.annotation.XmlAccessType;
  23 import javax.xml.bind.annotation.XmlAccessorType;
  24 import javax.xml.bind.annotation.XmlElement;
  25 import javax.xml.bind.annotation.XmlElementWrapper;
  26 import javax.xml.bind.annotation.XmlIDREF;
  27 import javax.xml.bind.annotation.XmlRootElement;
  28 import javax.xml.bind.annotation.XmlSchemaType;
  29 import javax.xml.bind.annotation.XmlType;
  30
  31 /**
  32  * @author m.doering
  33  * @version 1.0
  34  * @created 08-Nov-2007 13:06:43
  35  */
  36 @XmlAccessorType(XmlAccessType.FIELD)
  37 @XmlType(name = "PhylogeneticTree", propOrder = {
  38         "usedSequences"
  39 })
  40 @XmlRootElement(name = "PhylogeneticTree")
  41 @Entity
  42 @Indexed(index = "eu.etaxonomy.cdm.model.media.Media")
  43 @Audited
  44 public class PhylogeneticTree extends ReferencedMedia {
  45         private static final long serialVersionUID = -7020182117362324067L;
  46         private static final  Logger logger = Logger.getLogger(PhylogeneticTree.class);
  47
  48         @XmlElementWrapper(name = "UsedSequences")
  49         @XmlElement(name = "UsedSequence")
  50     @XmlIDREF
  51     @XmlSchemaType(name = "IDREF")
  52     @OneToMany(fetch = FetchType.LAZY)
  53         private Set<Sequence> usedSequences = new HashSet<Sequence>();
  54
  55         public Set<Sequence> getUsedSequences() {
  56                 logger.debug("getUsedSequences");
  57                 return usedSequences;
  58         }
  59
  60         public void addUsedSequences(Sequence usedSequence) {
  61                 this.usedSequences.add(usedSequence);
  62         }
  63
  64         public void removeUsedSequences(Sequence usedSequence) {
  65                 this.usedSequences.remove(usedSequence);
  66         }
  67 }