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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.description;
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import java.rmi.UnexpectedException;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import javax.persistence.Column;
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import javax.persistence.Entity;
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import javax.persistence.FetchType;
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import javax.persistence.OneToMany;
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import javax.persistence.OneToOne;
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import javax.persistence.Transient;
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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.XmlAttribute;
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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.XmlRootElement;
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import javax.xml.bind.annotation.XmlType;
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import org.apache.log4j.Logger;
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import org.hibernate.annotations.Cascade;
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import org.hibernate.annotations.CascadeType;
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import org.hibernate.annotations.Type;
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import org.hibernate.envers.Audited;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.term.DefinedTermBase;
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import eu.etaxonomy.cdm.model.term.IHasTermType;
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import eu.etaxonomy.cdm.model.term.Representation;
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import eu.etaxonomy.cdm.model.term.TermType;
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import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
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/**
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* The class to arrange {@link Feature features} (characters) in a tree structure.
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* Feature trees are essential as interactive multiple-access keys for
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* determination process and for systematical output arrangement of
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* {@link DescriptionElementBase description elements} according to different goals
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* but may also be used to define flat feature subsets for filtering purposes.<BR>
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* A feature tree is build on {@link FeatureNode feature nodes}.
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* <P>
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* This class corresponds partially to ConceptTreeDefType according to the SDD
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* schema.
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* <P>
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* Note: The tree structure of features used for purposes described above has
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* nothing in common with the possible hierarchical structure of features
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* depending on their grade of precision.
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*
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* @see MediaKey
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*
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* @author m.doering
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* @since 08-Nov-2007 13:06:16
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "FeatureTree", propOrder = {
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"root",
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"termType",
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"allowDuplicates",
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"representations"
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})
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@XmlRootElement(name = "FeatureTree")
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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.description.FeatureTree")
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@Audited
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public class FeatureTree <T extends DefinedTermBase>
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extends IdentifiableEntity<IIdentifiableEntityCacheStrategy>
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implements IHasTermType, Cloneable{
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private static final long serialVersionUID = -6713834139003172735L;
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private static final Logger logger = Logger.getLogger(FeatureTree.class);
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@XmlElement(name = "Root")
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@OneToOne(fetch = FetchType.LAZY, targetEntity=FeatureNode.class)
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private FeatureNode<T> root;
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/**
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* The {@link TermType type} of this term collection. All nodes in the graph must refer to a term of the same type.
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*/
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@XmlAttribute(name ="TermType")
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@Column(name="termType")
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@NotNull
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@Type(type = "eu.etaxonomy.cdm.hibernate.EnumUserType",
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parameters = {@org.hibernate.annotations.Parameter(name = "enumClass", value = "eu.etaxonomy.cdm.model.common.TermType")}
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)
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@Audited
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private TermType termType;
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// TODO needed? FeatureTree was a TermBase until v3.3 but was removed from
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//it as TermBase got the termType which does not apply to FeatureTree.
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//We need to check how far representations and uri is still required
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//or can be deleted. Current implementations seem all to use the title cache
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//instead of representation. This may not be correct.
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@XmlElementWrapper(name = "Representations")
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@XmlElement(name = "Representation")
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@OneToMany(fetch=FetchType.EAGER, orphanRemoval=true)
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@Cascade( { CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
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// @IndexedEmbedded no need for embedding since we are using the DefinedTermBaseClassBridge
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private Set<Representation> representations = new HashSet<>();
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//make them private for now as we may delete representations in future
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//otherwise if we decide to use representations we can make the getters public
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private Set<Representation> getRepresentations() {return representations;}
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private void setRepresentations(Set<Representation> representations) {this.representations = representations;}
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//#7372 indicates if this tree/graph allows duplicated terms/features
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private boolean allowDuplicates = false;
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//******************** FACTORY METHODS ******************************************/
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/**
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* Creates a new term collection instance for the given term type
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* with an empty {@link #getRoot() root node}.
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* @param termType the {@link TermType term type}, must not be null
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*/
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public static <T extends DefinedTermBase<T>> FeatureTree<T> NewInstance(@NotNull TermType termType){
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return new FeatureTree<>(termType);
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}
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/**
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* Creates a new feature tree instance with an empty {@link #getRoot() root node}.
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*
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* @see #NewInstance(UUID)
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* @see #NewInstance(List)
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*/
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public static FeatureTree<Feature> NewInstance(){
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return new FeatureTree<>(TermType.Feature);
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}
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/**
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* Creates a new feature tree instance with an empty {@link #getRoot() root node}
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* and assigns to the new feature tree the given
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* UUID (universally unique identifier).
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*
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* @param uuid the universally unique identifier
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* @see #NewInstance()
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* @see #NewInstance(List)
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*/
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public static <T extends DefinedTermBase<T>> FeatureTree<T> NewInstance(UUID uuid){
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FeatureTree<T> result = new FeatureTree<>(TermType.Feature);
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result.setUuid(uuid);
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return result;
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}
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/**
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* Creates a new feature tree instance with a {@link #getRoot() root node}
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* the children of which are the feature nodes build on the base of the
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* given list of {@link Feature features}. This corresponds to a flat feature tree.
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* For each feature within the list a new {@link FeatureNode feature node} without
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* children nodes will be created.
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*
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* @param featureList the feature list
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* @see #NewInstance()
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* @see #NewInstance(UUID)
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*/
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public static FeatureTree<Feature> NewInstance(List<Feature> featureList){
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FeatureTree<Feature> result = new FeatureTree<>(TermType.Feature);
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FeatureNode<Feature> root = result.getRoot();
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for (Feature feature : featureList){
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FeatureNode<Feature> child = FeatureNode.NewInstance(feature);
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root.addChild(child);
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}
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return result;
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}
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// ******************** CONSTRUCTOR *************************************/
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//for JAXB only, TODO needed?
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@Deprecated
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protected FeatureTree(){}
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/**
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* Class constructor: creates a new feature tree instance with an empty
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* {@link #getRoot() root node}.
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*/
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protected FeatureTree(TermType termType) {
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this.termType = termType;
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checkTermType(this);
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root = FeatureNode.NewInstance(termType);
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root.setFeatureTree(this);
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}
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// ****************** GETTER / SETTER **********************************/
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@Override
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public TermType getTermType() {
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return termType;
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}
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/**
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* Returns the topmost {@link FeatureNode feature node} (root node) of <i>this</i>
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* feature tree. The root node does not have any parent. Since feature nodes
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* recursively point to their child nodes the complete feature tree is
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* defined by its root node.
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*/
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public FeatureNode<T> getRoot() {
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return root;
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}
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/**
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* @deprecated this method is only for internal use when deleting a {@link FeatureTree}
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* from a database. It should never be called for other reasons.
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*/
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@Deprecated
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public void removeRootNode() {
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this.root = null;
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}
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/**
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* Returns the (ordered) list of {@link FeatureNode feature nodes} which are immediate
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* children of the root node of <i>this</i> feature tree.
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*/
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@Transient
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public List<FeatureNode<T>> getRootChildren(){
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List<FeatureNode<T>> result = new ArrayList<>();
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result.addAll(root.getChildNodes());
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return result;
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}
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public boolean isAllowDuplicates() {
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return allowDuplicates;
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}
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public void setAllowDuplicates(boolean allowDuplicates) {
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this.allowDuplicates = allowDuplicates;
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}
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/**
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* Throws {@link IllegalArgumentException} if the given
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* term has not the same term type as this term or if term type is null.
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* @param term
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*/
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private void checkTermType(IHasTermType term) {
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IHasTermType.checkTermTypes(term, this);
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}
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//******************** METHODS ***********************************************/
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/**
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* Computes a set of distinct terms that are present in this feature tree
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*
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* @return
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*/
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@Transient
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public Set<T> getDistinctFeatures(){
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if(termType.equals(TermType.Feature) || termType.isKindOf(TermType.Feature)){
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Set<T> features = new HashSet<>();
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return root.getDistinctFeaturesRecursive(features);
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}
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String message = "FeatureTree is not of type FEATURE.";
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logger.warn(message, new UnexpectedException(message));
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return new HashSet<>();
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}
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//*********************** CLONE ********************************************************/
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/**
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* Clones <i>this</i> FeatureTree. This is a shortcut that enables to create
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* a new instance that differs only slightly from <i>this</i> FeatureTree by
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* modifying only some of the attributes.
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* FeatureNodes always belong only to one tree, so all FeatureNodes are cloned to build
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* the new FeatureTree
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*
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*
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* @see eu.etaxonomy.cdm.model.term.TermBase#clone()
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* @see java.lang.Object#clone()
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*/
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@Override
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public Object clone() {
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FeatureTree<T> result;
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try {
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result = (FeatureTree<T>)super.clone();
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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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FeatureNode<T> rootClone = this.getRoot().cloneDescendants();
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result.root = rootClone;
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return result;
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}
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}
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