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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.model.molecular;
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import java.util.HashSet;
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import java.util.Set;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.ManyToMany;
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import javax.validation.constraints.NotNull;
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import javax.xml.bind.annotation.XmlAccessType;
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import javax.xml.bind.annotation.XmlAccessorType;
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import javax.xml.bind.annotation.XmlElement;
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import javax.xml.bind.annotation.XmlElementWrapper;
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import javax.xml.bind.annotation.XmlIDREF;
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import javax.xml.bind.annotation.XmlRootElement;
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import javax.xml.bind.annotation.XmlSchemaType;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.logging.log4j.LogManager;
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import org.apache.logging.log4j.Logger;
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import org.hibernate.envers.Audited;
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import eu.etaxonomy.cdm.model.media.Media;
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/**
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* "A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the
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* inferred evolutionary relationships among various biological species or other entities
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* based upon similarities and differences in their physical and/or genetic characteristics.
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* The taxa joined together in the tree are implied to have descended from a common ancestor."
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* (Wikipedia).
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* <BR> In the CDM we currently store phylogenetic trees only as media. This may change in future.
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*
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* @author m.doering
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* @since 08-Nov-2007
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "PhylogeneticTree", propOrder = {
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"usedSequences"
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})
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@XmlRootElement(name = "PhylogeneticTree")
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@Entity
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//@Indexed disabled to reduce clutter in indexes, since this type is not used by any search
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//@Indexed(index = "eu.etaxonomy.cdm.model.media.Media")
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@Audited
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public class PhylogeneticTree extends Media {
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private static final long serialVersionUID = -7020182117362324067L;
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private static final Logger logger = LogManager.getLogger();
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@XmlElementWrapper(name = "UsedSequences")
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@XmlElement(name = "UsedSequence")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToMany(fetch = FetchType.LAZY)
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@NotNull
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private Set<Sequence> usedSequences = new HashSet<Sequence>();
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//********************** Factory Method **********************************/
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/**
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* Factory method
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* @return
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*/
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public static PhylogeneticTree NewInstance(){
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return new PhylogeneticTree();
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}
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//***************** Constructor ****************************/
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private PhylogeneticTree(){
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super();
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}
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// ********************** GETTER / SETTER **************************/
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public Set<Sequence> getUsedSequences() {
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if(usedSequences == null) {
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this.usedSequences = new HashSet<Sequence>();
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}
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return usedSequences;
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}
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public void addUsedSequences(Sequence usedSequence) {
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this.usedSequences.add(usedSequence);
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}
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public void removeUsedSequences(Sequence usedSequence) {
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this.usedSequences.remove(usedSequence);
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}
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//*********** CLONE **********************************/
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/**
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* Clones <i>this</i> phylogenetic tree. This is a shortcut that enables to
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* create a new instance that differs only slightly from <i>this</i> phylogenetic tree
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* by modifying only some of the attributes.<BR>
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* This method overrides the clone method from {@link Media Media}.
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*
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* @see eu.etaxonomy.cdm.model.media.Media#clone()
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* @see java.lang.Object#clone()
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*/
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@Override
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public PhylogeneticTree clone(){
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PhylogeneticTree result;
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try{
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result= (PhylogeneticTree) super.clone();
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result.usedSequences = new HashSet<Sequence>();
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for (Sequence seq: this.usedSequences){
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result.addUsedSequences(seq.clone());
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}
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return result;
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}catch (CloneNotSupportedException e) {
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logger.warn("Object does not implement cloneable");
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e.printStackTrace();
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return null;
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}
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}
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}
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