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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.io.PrintStream;
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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.JoinColumn;
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import javax.persistence.JoinTable;
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import javax.persistence.ManyToMany;
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import javax.persistence.OneToOne;
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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.commons.lang.StringUtils;
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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.envers.Audited;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.IIntextReferenceTarget;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.strategy.cache.description.PolytomousKeyDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGenerator;
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/**
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* This class represents a fixed single-access key (dichotomous or
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* polytomous) used to identify (assign a {@link Taxon taxon} to) a {@link SpecimenOrObservationBase
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* specimen or observation}. The key may be written manually or may be generated automatically
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* e.g. by the {@link PolytomousKeyGenerator}. The different paths to the taxa are expressed
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* by a decision graph consisting of {@link PolytomousKeyNode
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* PolytomousKeyNodes}. The root node of such graph is accessible by
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* {@link #getRoot()}. Refer to {@link PolytomousKeyNode} for detailed
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* documentation on the decision graph structure.
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*
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* @author h.fradin
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* @created 13.08.2009
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*
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* @author a.mueller
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* @version 2.0 (08.11.2010)
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*/
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@XmlAccessorType(XmlAccessType.FIELD)
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@XmlType(name = "PolytomousKey", propOrder = {
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"coveredTaxa",
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"taxonomicScope",
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"geographicalScope",
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"scopeRestrictions",
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"root",
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"startNumber"})
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@XmlRootElement(name = "PolytomousKey")
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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.PolytomousKey")
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@Audited
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public class PolytomousKey
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extends IdentifiableEntity<PolytomousKeyDefaultCacheStrategy>
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implements IIdentificationKey, IIntextReferenceTarget {
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private static final long serialVersionUID = -3368243754557343942L;
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private static final Logger logger = Logger.getLogger(PolytomousKey.class);
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@XmlElementWrapper(name = "CoveredTaxa")
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@XmlElement(name = "CoveredTaxon")
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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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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private Set<Taxon> coveredTaxa = new HashSet<Taxon>();
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@XmlElementWrapper(name = "TaxonomicScope")
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@XmlElement(name = "Taxon")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name = "PolytomousKey_Taxon",
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joinColumns = @JoinColumn(name = "polytomousKey_id"),
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inverseJoinColumns = @JoinColumn(name = "taxon_id")
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)
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@NotNull
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@Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
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private Set<Taxon> taxonomicScope = new HashSet<Taxon>();
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@XmlElementWrapper(name = "GeographicalScope")
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@XmlElement(name = "Area")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name = "PolytomousKey_NamedArea")
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@NotNull
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// @Cascade({CascadeType.MERGE}) remove cascade #5755
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private Set<NamedArea> geographicalScope = new HashSet<NamedArea>();
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@XmlElementWrapper(name = "ScopeRestrictions")
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@XmlElement(name = "Restriction")
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@XmlIDREF
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@XmlSchemaType(name = "IDREF")
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@ManyToMany(fetch = FetchType.LAZY)
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@JoinTable(name = "PolytomousKey_Scope")
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@NotNull
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// @Cascade({CascadeType.MERGE}) remove cascade #5755
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private Set<DefinedTerm> scopeRestrictions = new HashSet<DefinedTerm>();
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@XmlElement(name = "Root")
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@OneToOne(fetch = FetchType.LAZY)
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@Cascade({ CascadeType.SAVE_UPDATE, CascadeType.MERGE })
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private PolytomousKeyNode root;
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@XmlElement(name = "StartNumber")
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@Audited
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private int startNumber = 1;
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// ***************** STATIC METHODS ********************************/
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/**
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* Creates a new empty identification multi-access key instance.
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*/
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public static PolytomousKey NewInstance() {
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return new PolytomousKey();
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}
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/**
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* Creates a new empty identification polytomous key instance.
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*/
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public static PolytomousKey NewTitledInstance(String title) {
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PolytomousKey result = new PolytomousKey();
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result.setTitleCache(title, true);
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return result;
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}
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// ************************** CONSTRUCTOR ************************/
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/**
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* Class constructor: creates a new empty multi-access key instance.
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*/
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protected PolytomousKey() {
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super();
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root = PolytomousKeyNode.NewInstance();
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root.setNodeNumber(getStartNumber());
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root.setKey(this);
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this.cacheStrategy = PolytomousKeyDefaultCacheStrategy.NewInstance();
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}
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// ************************ GETTER/ SETTER
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/**
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* Returns the topmost {@link PolytomousKeyNode polytomous key node} (root
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* node) of <i>this</i> polytomous key. The root node does not have any
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* parent. Since polytomous key nodes recursively point to their child nodes
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* the complete polytomous key is defined by its root node.
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*/
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public PolytomousKeyNode getRoot() {
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return root;
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}
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/**
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* This method should be used by Hibernate only. If we want to make this
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* method public we have to think about biderionality and also what should
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* happen with the old root node.
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*
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* @see #getRoot()
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*/
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public void setRoot(PolytomousKeyNode root) {
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this.root = root;
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if (root != null){
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root.setKey(this);
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}
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}
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/**
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* Returns the set of possible {@link Taxon taxa} corresponding to
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* <i>this</i> identification key.
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*/
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@Override
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public Set<Taxon> getCoveredTaxa() {
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if (coveredTaxa == null) {
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this.coveredTaxa = new HashSet<Taxon>();
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}
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return coveredTaxa;
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}
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/**
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* @see #getCoveredTaxa()
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*/
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protected void setCoveredTaxa(Set<Taxon> coveredTaxa) {
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this.coveredTaxa = coveredTaxa;
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}
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/**
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* Adds a {@link Taxon taxa} to the set of {@link #getCoveredTaxa() covered
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* taxa} corresponding to <i>this</i> identification key.
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*
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* @param taxon
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* the taxon to be added to <i>this</i> identification key
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* @see #getCoveredTaxa()
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*/
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@Override
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public void addCoveredTaxon(Taxon taxon) {
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this.coveredTaxa.add(taxon);
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}
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/**
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* Removes one element from the set of {@link #getCoveredTaxa() covered
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* taxa} corresponding to <i>this</i> identification key.
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*
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* @param taxon
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* the taxon which should be removed
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* @see #getCoveredTaxa()
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* @see #addCoveredTaxon(Taxon)
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*/
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@Override
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public void removeCoveredTaxon(Taxon taxon) {
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this.coveredTaxa.remove(taxon);
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}
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/**
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* Returns the set of {@link NamedArea named areas} indicating the
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* geospatial data where <i>this</i> identification key is valid.
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*/
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@Override
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public Set<NamedArea> getGeographicalScope() {
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if (geographicalScope == null) {
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this.geographicalScope = new HashSet<NamedArea>();
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}
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return geographicalScope;
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}
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/**
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* Adds a {@link NamedArea geoScope} to the set of {@link #getGeoScopes()
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* geogspatial scopes} corresponding to <i>this</i> identification key.
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*
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* @param geoScope
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* the named area to be added to <i>this</i> identification key
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* @see #getGeoScopes()
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*/
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@Override
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public void addGeographicalScope(NamedArea geoScope) {
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this.geographicalScope.add(geoScope);
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}
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/**
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* Removes one element from the set of {@link #getGeoScopes() geogspatial
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* scopes} corresponding to <i>this</i> identification key.
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*
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* @param geoScope
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* the named area which should be removed
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* @see #getGeoScopes()
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* @see #addGeoScope(NamedArea)
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*/
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@Override
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public void removeGeographicalScope(NamedArea geoScope) {
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this.geographicalScope.remove(geoScope);
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}
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/**
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* Returns the set of {@link Taxon taxa} that define the taxonomic scope of
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* <i>this</i> identification key
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*/
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@Override
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public Set<Taxon> getTaxonomicScope() {
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if (taxonomicScope == null) {
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this.taxonomicScope = new HashSet<Taxon>();
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}
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return taxonomicScope;
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}
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/**
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* Adds a {@link Taxon taxa} to the set of {@link #getTaxonomicScope()
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* taxonomic scopes} corresponding to <i>this</i> identification key.
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*
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* @param taxon
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* the taxon to be added to <i>this</i> identification key
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* @see #getTaxonomicScope()
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*/
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@Override
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public void addTaxonomicScope(Taxon taxon) {
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this.taxonomicScope.add(taxon);
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}
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/**
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* Removes one element from the set of {@link #getTaxonomicScope() taxonomic
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* scopes} corresponding to <i>this</i> identification key.
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*
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* @param taxon
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* the taxon which should be removed
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* @see #getTaxonomicScope()
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* @see #addTaxonomicScope(Taxon)
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*/
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@Override
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public void removeTaxonomicScope(Taxon taxon) {
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this.taxonomicScope.remove(taxon);
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}
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/**
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* Returns the set of {@link Scope scope restrictions} corresponding to
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* <i>this</i> identification key
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*/
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@Override
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public Set<DefinedTerm> getScopeRestrictions() {
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if (scopeRestrictions == null) {
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this.scopeRestrictions = new HashSet<DefinedTerm>();
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}
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return scopeRestrictions;
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}
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/**
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* Adds a {@link Scope scope restriction} to the set of
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* {@link #getScopeRestrictions() scope restrictions} corresponding to
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* <i>this</i> identification key.
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*
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* @param scopeRestriction
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* the scope restriction to be added to <i>this</i>
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* identification key
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* @see #getScopeRestrictions()
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*/
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@Override
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public void addScopeRestriction(DefinedTerm scopeRestriction) {
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this.scopeRestrictions.add(scopeRestriction);
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}
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/**
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* Removes one element from the set of {@link #getScopeRestrictions() scope
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* restrictions} corresponding to <i>this</i> identification key.
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*
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* @param scopeRestriction
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* the scope restriction which should be removed
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* @see #getScopeRestrictions()
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* @see #addScopeRestriction(Scope)
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*/
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@Override
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public void removeScopeRestriction(DefinedTerm scopeRestriction) {
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this.scopeRestrictions.remove(scopeRestriction);
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}
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/**
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* The first number for the automated numbering of {@link PolytomousKeyNode key nodes}.
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* Default value is 1.
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* @return
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*/
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public int getStartNumber() {
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return startNumber;
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}
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/**
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* @see #getStartNumber()
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* @param startNumber
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*/
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public void setStartNumber(int startNumber) {
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this.startNumber = startNumber;
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}
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// ******************** toString *****************************************/
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private class IntegerObject {
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int number = 0;
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int inc() {
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return number++;
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};
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@Override
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public String toString() {
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return String.valueOf(number);
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}
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}
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public String print(PrintStream stream) {
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String title = this.getTitleCache() + "\n";
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String strPrint = title;
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if (stream != null) {
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stream.print(title);
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}
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PolytomousKeyNode root = this.getRoot();
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strPrint += printNode(root, null, " ", stream);
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return strPrint;
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}
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/**
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* TODO this is a preliminary implementation
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*
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* @param node
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* @param identation
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* @param no
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* @param myNumber
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* @param stream
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* @return
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*/
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private String printNode(PolytomousKeyNode node, PolytomousKeyNode parent2,
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String identation, PrintStream stream) {
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String separator = ", ";
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String result = identation + node.getNodeNumber() + ". ";
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if (node != null) {
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// key choice
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String question = null;
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String feature = null;
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if (node.getQuestion() != null) {
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question = node.getQuestion().getLabelText(Language.DEFAULT());
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}
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if (node.getFeature() != null) {
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feature = node.getFeature().getLabel(Language.DEFAULT());
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}
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result += CdmUtils.concat(" - ", question, feature) + "\n";
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;
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// Leads
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char nextCounter = 'a';
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for (PolytomousKeyNode child : node.getChildren()) {
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String leadNumber = String.valueOf(nextCounter++);
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if (child.getStatement() != null) {
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String statement = child.getStatement().getLabelText(
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Language.DEFAULT());
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result += identation + " " + leadNumber + ") "
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+ (statement == null ? "" : (statement));
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result += " ... ";
|
443
|
// child node
|
444
|
if (!child.isLeaf()) {
|
445
|
result += child.getNodeNumber() + separator;
|
446
|
}
|
447
|
// taxon
|
448
|
if (child.getTaxon() != null) {
|
449
|
String strTaxon = "";
|
450
|
if (child.getTaxon().getName() != null) {
|
451
|
strTaxon = child.getTaxon().getName()
|
452
|
.getTitleCache();
|
453
|
} else {
|
454
|
strTaxon = child.getTaxon().getTitleCache();
|
455
|
}
|
456
|
result += strTaxon + separator;
|
457
|
}
|
458
|
// subkey
|
459
|
if (child.getSubkey() != null) {
|
460
|
String subkey = child.getSubkey().getTitleCache();
|
461
|
result += subkey + separator;
|
462
|
}
|
463
|
// other node
|
464
|
if (child.getOtherNode() != null) {
|
465
|
PolytomousKeyNode otherNode = child.getOtherNode();
|
466
|
String otherNodeString = null;
|
467
|
if (child.getKey().equals(otherNode.getKey())) {
|
468
|
otherNodeString = String.valueOf(otherNode
|
469
|
.getNodeNumber());
|
470
|
} else {
|
471
|
otherNodeString = otherNode.getKey() + " "
|
472
|
+ otherNode.getNodeNumber();
|
473
|
}
|
474
|
result += otherNodeString + separator;
|
475
|
}
|
476
|
|
477
|
result = StringUtils.chomp(result, separator);
|
478
|
result += "\n";
|
479
|
}
|
480
|
}
|
481
|
|
482
|
if (stream != null) {
|
483
|
stream.print(result);
|
484
|
}
|
485
|
for (PolytomousKeyNode child : node.getChildren()) {
|
486
|
if (!child.isLeaf()) {
|
487
|
result += printNode(child, node, identation + "", stream);
|
488
|
}
|
489
|
}
|
490
|
}
|
491
|
return result;
|
492
|
}
|
493
|
|
494
|
//
|
495
|
// public List<PolytomousKeyNode> getChildren() {
|
496
|
// return getRoot().getChildren();
|
497
|
// }
|
498
|
|
499
|
// *********************** CLONE ************************************/
|
500
|
|
501
|
/**
|
502
|
* Clones <i>this</i> PolytomousKey. This is a shortcut that enables to
|
503
|
* create a new instance that differs only slightly from <i>this</i>
|
504
|
* PolytomousKey by modifying only some of the attributes.
|
505
|
*
|
506
|
* @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#clone()
|
507
|
* @see java.lang.Object#clone()
|
508
|
*/
|
509
|
@Override
|
510
|
public Object clone() {
|
511
|
PolytomousKey result;
|
512
|
|
513
|
try {
|
514
|
result = (PolytomousKey) super.clone();
|
515
|
|
516
|
result.coveredTaxa = new HashSet<Taxon>();
|
517
|
for (Taxon taxon : this.coveredTaxa) {
|
518
|
result.addCoveredTaxon(taxon);
|
519
|
}
|
520
|
|
521
|
result.geographicalScope = new HashSet<NamedArea>();
|
522
|
for (NamedArea area : this.geographicalScope) {
|
523
|
result.addGeographicalScope(area);
|
524
|
}
|
525
|
|
526
|
result.root = (PolytomousKeyNode) this.root.clone();
|
527
|
|
528
|
result.scopeRestrictions = new HashSet<DefinedTerm>();
|
529
|
for (DefinedTerm scope : this.scopeRestrictions) {
|
530
|
result.addScopeRestriction(scope);
|
531
|
}
|
532
|
|
533
|
result.taxonomicScope = new HashSet<Taxon>();
|
534
|
for (Taxon taxon : this.taxonomicScope) {
|
535
|
result.addTaxonomicScope(taxon);
|
536
|
}
|
537
|
|
538
|
return result;
|
539
|
|
540
|
} catch (CloneNotSupportedException e) {
|
541
|
logger.warn("Object does not implement cloneable");
|
542
|
e.printStackTrace();
|
543
|
return null;
|
544
|
}
|
545
|
|
546
|
}
|
547
|
|
548
|
}
|