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 java.util.HashSet;
  14 import java.util.Set;
  15
  16 import javax.persistence.Entity;
  17 import javax.persistence.FetchType;
  18 import javax.persistence.ManyToMany;
  19 import javax.validation.constraints.NotNull;
  20 import javax.xml.bind.annotation.XmlAccessType;
  21 import javax.xml.bind.annotation.XmlAccessorType;
  22 import javax.xml.bind.annotation.XmlElement;
  23 import javax.xml.bind.annotation.XmlElementWrapper;
  24 import javax.xml.bind.annotation.XmlIDREF;
  25 import javax.xml.bind.annotation.XmlRootElement;
  26 import javax.xml.bind.annotation.XmlSchemaType;
  27 import javax.xml.bind.annotation.XmlType;
  28
  29 import org.apache.log4j.Logger;
  30 import org.hibernate.envers.Audited;
  31 import org.hibernate.search.annotations.Indexed;
  32
  33 import eu.etaxonomy.cdm.model.media.Media;
  34
  35 /**
  36  * "A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the
  37  * inferred evolutionary relationships among various biological species or other entities
  38  * based upon similarities and differences in their physical and/or genetic characteristics.
  39  * The taxa joined together in the tree are implied to have descended from a common ancestor."
  40  * (Wikipedia).
  41  * <BR> In the CDM we currently store phylogenetic trees only as media. This may change in future.
  42  *
  43  * @author m.doering
  44  * @created 08-Nov-2007
  45  */
  46 @XmlAccessorType(XmlAccessType.FIELD)
  47 @XmlType(name = "PhylogeneticTree", propOrder = {
  48         "usedSequences"
  49 })
  50 @XmlRootElement(name = "PhylogeneticTree")
  51 @Entity
  52 @Indexed(index = "eu.etaxonomy.cdm.model.media.Media")
  53 @Audited
  54 public class PhylogeneticTree extends Media implements Cloneable{
  55         private static final long serialVersionUID = -7020182117362324067L;
  56         private static final  Logger logger = Logger.getLogger(PhylogeneticTree.class);
  57
  58
  59         @XmlElementWrapper(name = "UsedSequences")
  60         @XmlElement(name = "UsedSequence")
  61     @XmlIDREF
  62     @XmlSchemaType(name = "IDREF")
  63     @ManyToMany(fetch = FetchType.LAZY)
  64     @NotNull
  65         private Set<Sequence> usedSequences = new HashSet<Sequence>();
  66
  67 //********************** Factory Method **********************************/
  68
  69     /**
  70      * Factory method
  71      * @return
  72      */
  73     public static PhylogeneticTree NewInstance(){
  74         return new PhylogeneticTree();
  75     }
  76
  77
  78 //***************** Constructor ****************************/
  79
  80     private PhylogeneticTree(){
  81         super();
  82     }
  83
  84
  85
  86 // ********************** GETTER / SETTER **************************/
  87
  88         public Set<Sequence> getUsedSequences() {
  89                 if(usedSequences == null) {
  90                         this.usedSequences = new HashSet<Sequence>();
  91                 }
  92                 return usedSequences;
  93         }
  94
  95         public void addUsedSequences(Sequence usedSequence) {
  96                 this.usedSequences.add(usedSequence);
  97         }
  98
  99         public void removeUsedSequences(Sequence usedSequence) {
 100                 this.usedSequences.remove(usedSequence);
 101
 102         }
 103
 104 //*********** CLONE **********************************/
 105
 106         /**
 107          * Clones <i>this</i> phylogenetic tree. This is a shortcut that enables to
 108          * create a new instance that differs only slightly from <i>this</i> phylogenetic tree
 109          * by modifying only some of the attributes.<BR>
 110          * This method overrides the clone method from {@link Media Media}.
 111          *
 112          * @see eu.etaxonomy.cdm.model.media.Media#clone()
 113          * @see java.lang.Object#clone()
 114          */
 115         @Override
 116
 117         public Object clone(){
 118                 PhylogeneticTree result;
 119                 try{
 120                         result= (PhylogeneticTree) super.clone();
 121                         result.usedSequences = new HashSet<Sequence>();
 122                         for (Sequence seq: this.usedSequences){
 123                                 result.addUsedSequences((Sequence)seq.clone());
 124                         }
 125
 126                         return result;
 127                 }catch (CloneNotSupportedException e) {
 128                         logger.warn("Object does not implement cloneable");
 129                         e.printStackTrace();
 130                         return null;
 131                 }
 132         }
 133 }