Revision af45e069
Added by Andreas Müller almost 8 years ago
cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/TypeDesignationBase.java | ||
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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.name; |
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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.Inheritance; |
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import javax.persistence.InheritanceType; |
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import javax.persistence.ManyToMany; |
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import javax.persistence.ManyToOne; |
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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.XmlSeeAlso; |
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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.envers.Audited; |
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import eu.etaxonomy.cdm.model.common.ReferencedEntityBase; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.validation.Level2; |
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import eu.etaxonomy.cdm.validation.annotation.ValidTypeDesignation; |
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/** |
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* The (abstract) class representing a typification of one or several {@link TaxonNameBase taxon names}.<BR> |
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* All taxon names which have a {@link Rank rank} "species aggregate" or lower |
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* can only be typified by specimens (a {@link SpecimenTypeDesignation specimen type designation}), but taxon |
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* names with a higher rank might be typified by an other taxon name with |
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* rank "species" or "genus" (a {@link NameTypeDesignation name type designation}). |
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* |
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* @see TaxonNameBase |
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* @see NameTypeDesignation |
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* @see SpecimenTypeDesignation |
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* @author a.mueller |
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* @created 07.08.2008 |
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* @version 1.0 |
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*/ |
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@XmlRootElement(name = "TypeDesignationBase") |
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@XmlType(name = "TypeDesignationBase", propOrder = { |
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"typifiedNames", |
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"notDesignated", |
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"typeStatus" |
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}) |
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@XmlSeeAlso({ |
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NameTypeDesignation.class, |
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SpecimenTypeDesignation.class |
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}) |
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@Entity |
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@Audited |
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@Inheritance(strategy=InheritanceType.SINGLE_TABLE) |
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@ValidTypeDesignation(groups=Level2.class) |
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public abstract class TypeDesignationBase<T extends TypeDesignationStatusBase> extends ReferencedEntityBase implements ITypeDesignation { |
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private static final long serialVersionUID = 8622351017235131355L; |
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@SuppressWarnings("unused") |
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private static final Logger logger = Logger.getLogger(TypeDesignationBase.class); |
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@XmlElement(name = "IsNotDesignated") |
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private boolean notDesignated; |
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@XmlElementWrapper(name = "TypifiedNames") |
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@XmlElement(name = "TypifiedName") |
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@XmlIDREF |
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@XmlSchemaType(name = "IDREF") |
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@ManyToMany(fetch = FetchType.LAZY , mappedBy="typeDesignations") |
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@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE}) |
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private Set<TaxonNameBase> typifiedNames = new HashSet<TaxonNameBase>(); |
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// @XmlElement(name = "HomotypicalGroup") |
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// @XmlIDREF |
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// @XmlSchemaType(name = "IDREF") |
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// @ManyToOne(fetch = FetchType.LAZY) |
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// @Cascade(CascadeType.SAVE_UPDATE,CascadeType.MERGE) |
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// private HomotypicalGroup homotypicalGroup; |
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@XmlElement(name = "TypeStatus") |
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@XmlIDREF |
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@XmlSchemaType(name = "IDREF") |
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@ManyToOne(fetch = FetchType.LAZY, targetEntity = TypeDesignationStatusBase.class) |
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private T typeStatus; |
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// **************** CONSTRUCTOR *************************************/ |
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/** |
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* Class constructor: creates a new empty type designation. |
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* |
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* @see #TypeDesignationBase(Reference, String, String, Boolean) |
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*/ |
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protected TypeDesignationBase(){ |
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super(); |
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} |
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/** |
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* Class constructor: creates a new type designation |
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* (including its {@link Reference reference source} and eventually |
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* the taxon name string originally used by this reference when establishing |
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* the former designation). |
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* |
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* @param citation the reference source for the new designation |
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* @param citationMicroReference the string with the details describing the exact localisation within the reference |
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* @param originalNameString the taxon name string used originally in the reference source for the new designation |
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* @see #TypeDesignationBase() |
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* @see #isNotDesignated() |
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* @see TaxonNameBase#getTypeDesignations() |
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*/ |
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protected TypeDesignationBase(Reference citation, String citationMicroReference, String originalNameString) { |
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this(citation, citationMicroReference, originalNameString, false); |
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} |
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/** |
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* Class constructor: creates a new type designation |
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* (including its {@link Reference reference source} and eventually |
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* the taxon name string originally used by this reference when establishing |
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* the former designation). |
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* |
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* @param citation the reference source for the new designation |
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* @param citationMicroReference the string with the details describing the exact localisation within the reference |
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* @param originalNameString the taxon name string used originally in the reference source for the new designation |
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* @param isNotDesignated the boolean flag indicating whether there is no type at all for |
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* <i>this</i> type designation |
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* @see #TypeDesignationBase() |
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* @see #isNotDesignated() |
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* @see TaxonNameBase#getTypeDesignations() |
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*/ |
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protected TypeDesignationBase(Reference citation, String citationMicroReference, String originalNameString, boolean notDesignated){ |
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super(citation, citationMicroReference, originalNameString); |
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this.notDesignated = notDesignated; |
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} |
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// **************** METHODS *************************************/ |
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/** |
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* Returns the {@link TypeDesignationStatusBase type designation status} for <i>this</i> specimen type |
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* designation. This status describes which of the possible categories of |
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* types like "holotype", "neotype", "syntype" or "isotype" applies to <i>this</i> |
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* specimen type designation. |
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*/ |
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public T getTypeStatus(){ |
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return this.typeStatus; |
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} |
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/** |
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* @see #getTypeStatus() |
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*/ |
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public void setTypeStatus(T typeStatus){ |
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this.typeStatus = typeStatus; |
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} |
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// /* (non-Javadoc) |
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// * @see eu.etaxonomy.cdm.model.name.ITypeDesignation#getHomotypicalGroup() |
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// */ |
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// /** |
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// * Returns the {@link HomotypicalGroup homotypical group} to which all (in <i>this</i> |
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// * type designation) typified {@link TaxonNameBase taxon names} belong. |
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// * |
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// * @see #getTypifiedNames() |
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// * @deprecated homotypical group can not be set and always seems to be <code>null</code>. |
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// * Probably it is a relict of an old version. |
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// * See also http://dev.e-taxonomy.eu/trac/ticket/2173 |
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// */ |
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// @Deprecated |
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// public HomotypicalGroup getHomotypicalGroup() { |
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// return homotypicalGroup; |
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// } |
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/* (non-Javadoc) |
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* @see eu.etaxonomy.cdm.model.name.ITypeDesignation#getTypifiedNames() |
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*/ |
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/** |
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* Returns the set of {@link TaxonNameBase taxon names} typified in <i>this</i> |
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* type designation. This is a subset of the taxon names belonging to the |
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* corresponding {@link #getHomotypicalGroup() homotypical group}. |
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*/ |
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@Override |
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public Set<TaxonNameBase> getTypifiedNames() { |
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return typifiedNames; |
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} |
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/** |
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* Returns the boolean value "true" if it is known that a type does not |
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* exist and therefore the {@link TaxonNameBase taxon name} to which <i>this</i> |
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* type designation is assigned must still be typified. Two |
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* cases must be differentiated: <BR><ul> |
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* <li> a) it is unknown whether a type exists and |
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* <li> b) it is known that no type exists |
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* </ul> |
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* If a) is true there should be no TypeDesignation instance at all |
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* assigned to the "typified" taxon name.<BR> |
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* If b) is true there should be a TypeDesignation instance with the |
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* flag isNotDesignated set. The typeName attribute, in case of a |
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* {@link NameTypeDesignation name type designation}, or the typeSpecimen attribute, |
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* in case of a {@link SpecimenTypeDesignation specimen type designation}, should then be "null". |
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*/ |
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public boolean isNotDesignated() { |
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return notDesignated; |
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} |
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/** |
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* @see #isNotDesignated() |
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*/ |
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public void setNotDesignated(boolean notDesignated) { |
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this.notDesignated = notDesignated; |
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} |
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/** |
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* @deprecated for bidirectional use only |
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*/ |
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@Deprecated |
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protected void addTypifiedName(TaxonNameBase taxonName){ |
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this.typifiedNames.add(taxonName); |
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} |
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/** |
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* @deprecated for bidirectional use only |
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*/ |
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@Deprecated |
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protected void removeTypifiedName(TaxonNameBase taxonName){ |
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this.typifiedNames.remove(taxonName); |
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if (taxonName.getTypeDesignations().contains(this)){ |
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taxonName.removeTypeDesignation(this); |
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} |
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} |
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public abstract void removeType(); |
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//*********************** CLONE ********************************************************/ |
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/** |
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* Clones <i>this</i> type designation. This is a shortcut that enables to create |
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* a new instance that differs only slightly from <i>this</i> type designation by |
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* modifying only some of the attributes.<BR> |
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* CAUTION: the typifiedNames set is not cloned but empty after cloning as the typified |
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* names is considered to be the not owning part of a bidirectional relationship. |
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* This may be changed in future. |
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* |
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* @throws CloneNotSupportedException |
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* |
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* @see eu.etaxonomy.cdm.model.common.ReferencedEntityBase#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() throws CloneNotSupportedException { |
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TypeDesignationBase result = (TypeDesignationBase)super.clone(); |
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result.typifiedNames = new HashSet<TaxonNameBase>(); |
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// for (TaxonNameBase taxonNameBase : getTypifiedNames()){ |
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// result.typifiedNames.add(taxonNameBase); |
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// } |
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//no changes to: notDesignated, typeStatus, homotypicalGroup |
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return result; |
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} |
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} |
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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.name; |
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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.Inheritance; |
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import javax.persistence.InheritanceType; |
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import javax.persistence.ManyToMany; |
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import javax.persistence.ManyToOne; |
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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.XmlSeeAlso; |
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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.envers.Audited; |
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import eu.etaxonomy.cdm.model.common.ReferencedEntityBase; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.validation.Level2; |
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import eu.etaxonomy.cdm.validation.annotation.ValidTypeDesignation; |
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/** |
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* The (abstract) class representing a typification of one or several {@link TaxonNameBase taxon names}.<BR> |
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* All taxon names which have a {@link Rank rank} "species aggregate" or lower |
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* can only be typified by specimens (a {@link SpecimenTypeDesignation specimen type designation}), but taxon |
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* names with a higher rank might be typified by an other taxon name with |
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* rank "species" or "genus" (a {@link NameTypeDesignation name type designation}). |
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* |
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* @see TaxonNameBase |
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* @see NameTypeDesignation |
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* @see SpecimenTypeDesignation |
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* @author a.mueller |
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* @created 07.08.2008 |
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* @version 1.0 |
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*/ |
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@XmlRootElement(name = "TypeDesignationBase") |
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@XmlType(name = "TypeDesignationBase", propOrder = { |
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"typifiedNames", |
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"notDesignated", |
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"typeStatus" |
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}) |
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@XmlSeeAlso({ |
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NameTypeDesignation.class, |
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SpecimenTypeDesignation.class |
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}) |
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@Entity |
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@Audited |
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@Inheritance(strategy=InheritanceType.SINGLE_TABLE) |
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@ValidTypeDesignation(groups=Level2.class) |
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public abstract class TypeDesignationBase<T extends TypeDesignationStatusBase> extends ReferencedEntityBase implements ITypeDesignation { |
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private static final long serialVersionUID = 8622351017235131355L; |
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@SuppressWarnings("unused") |
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private static final Logger logger = Logger.getLogger(TypeDesignationBase.class); |
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@XmlElement(name = "IsNotDesignated") |
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private boolean notDesignated; |
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@XmlElementWrapper(name = "TypifiedNames") |
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@XmlElement(name = "TypifiedName") |
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@XmlIDREF |
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@XmlSchemaType(name = "IDREF") |
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@ManyToMany(fetch = FetchType.LAZY , mappedBy="typeDesignations") |
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@Cascade({CascadeType.SAVE_UPDATE,CascadeType.MERGE}) |
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private Set<TaxonNameBase> typifiedNames = new HashSet<TaxonNameBase>(); |
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@XmlElement(name = "TypeStatus") |
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@XmlIDREF |
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@XmlSchemaType(name = "IDREF") |
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@ManyToOne(fetch = FetchType.LAZY, targetEntity = TypeDesignationStatusBase.class) |
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private T typeStatus; |
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// **************** CONSTRUCTOR *************************************/ |
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/** |
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* Class constructor: creates a new empty type designation. |
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* |
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* @see #TypeDesignationBase(Reference, String, String, Boolean) |
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*/ |
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protected TypeDesignationBase(){ |
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super(); |
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} |
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/** |
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* Class constructor: creates a new type designation |
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* (including its {@link Reference reference source} and eventually |
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* the taxon name string originally used by this reference when establishing |
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* the former designation). |
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* |
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* @param citation the reference source for the new designation |
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* @param citationMicroReference the string with the details describing the exact localisation within the reference |
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* @param originalNameString the taxon name string used originally in the reference source for the new designation |
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* @see #TypeDesignationBase() |
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* @see #isNotDesignated() |
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* @see TaxonNameBase#getTypeDesignations() |
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*/ |
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protected TypeDesignationBase(Reference citation, String citationMicroReference, String originalNameString) { |
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this(citation, citationMicroReference, originalNameString, false); |
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} |
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/** |
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* Class constructor: creates a new type designation |
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* (including its {@link Reference reference source} and eventually |
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* the taxon name string originally used by this reference when establishing |
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* the former designation). |
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* |
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* @param citation the reference source for the new designation |
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* @param citationMicroReference the string with the details describing the exact localisation within the reference |
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* @param originalNameString the taxon name string used originally in the reference source for the new designation |
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* @param isNotDesignated the boolean flag indicating whether there is no type at all for |
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* <i>this</i> type designation |
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* @see #TypeDesignationBase() |
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* @see #isNotDesignated() |
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* @see TaxonNameBase#getTypeDesignations() |
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*/ |
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protected TypeDesignationBase(Reference citation, String citationMicroReference, String originalNameString, boolean notDesignated){ |
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super(citation, citationMicroReference, originalNameString); |
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this.notDesignated = notDesignated; |
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} |
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// **************** METHODS *************************************/ |
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/** |
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* Returns the {@link TypeDesignationStatusBase type designation status} for <i>this</i> specimen type |
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* designation. This status describes which of the possible categories of |
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* types like "holotype", "neotype", "syntype" or "isotype" applies to <i>this</i> |
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* specimen type designation. |
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*/ |
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public T getTypeStatus(){ |
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return this.typeStatus; |
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} |
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/** |
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* @see #getTypeStatus() |
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*/ |
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public void setTypeStatus(T typeStatus){ |
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this.typeStatus = typeStatus; |
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} |
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|
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/** |
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* Returns the set of {@link TaxonNameBase taxon names} typified in <i>this</i> |
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* type designation. This is a subset of the taxon names belonging to the |
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* corresponding {@link #getHomotypicalGroup() homotypical group}. |
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*/ |
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@Override |
|
164 |
public Set<TaxonNameBase> getTypifiedNames() { |
|
165 |
return typifiedNames; |
|
166 |
} |
|
167 |
|
|
168 |
/** |
|
169 |
* Returns the boolean value "true" if it is known that a type does not |
|
170 |
* exist and therefore the {@link TaxonNameBase taxon name} to which <i>this</i> |
|
171 |
* type designation is assigned must still be typified. Two |
|
172 |
* cases must be differentiated: <BR><ul> |
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173 |
* <li> a) it is unknown whether a type exists and |
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174 |
* <li> b) it is known that no type exists |
|
175 |
* </ul> |
|
176 |
* If a) is true there should be no TypeDesignation instance at all |
|
177 |
* assigned to the "typified" taxon name.<BR> |
|
178 |
* If b) is true there should be a TypeDesignation instance with the |
|
179 |
* flag isNotDesignated set. The typeName attribute, in case of a |
|
180 |
* {@link NameTypeDesignation name type designation}, or the typeSpecimen attribute, |
|
181 |
* in case of a {@link SpecimenTypeDesignation specimen type designation}, should then be "null". |
|
182 |
*/ |
|
183 |
public boolean isNotDesignated() { |
|
184 |
return notDesignated; |
|
185 |
} |
|
186 |
|
|
187 |
/** |
|
188 |
* @see #isNotDesignated() |
|
189 |
*/ |
|
190 |
public void setNotDesignated(boolean notDesignated) { |
|
191 |
this.notDesignated = notDesignated; |
|
192 |
} |
|
193 |
|
|
194 |
/** |
|
195 |
* @deprecated for bidirectional use only |
|
196 |
*/ |
|
197 |
@Deprecated |
|
198 |
protected void addTypifiedName(TaxonNameBase taxonName){ |
|
199 |
this.typifiedNames.add(taxonName); |
|
200 |
} |
|
201 |
|
|
202 |
/** |
|
203 |
* @deprecated for bidirectional use only |
|
204 |
*/ |
|
205 |
@Deprecated |
|
206 |
protected void removeTypifiedName(TaxonNameBase taxonName){ |
|
207 |
this.typifiedNames.remove(taxonName); |
|
208 |
if (taxonName.getTypeDesignations().contains(this)){ |
|
209 |
taxonName.removeTypeDesignation(this); |
|
210 |
} |
|
211 |
} |
|
212 |
|
|
213 |
public abstract void removeType(); |
|
214 |
|
|
215 |
//*********************** CLONE ********************************************************/ |
|
216 |
|
|
217 |
/** |
|
218 |
* Clones <i>this</i> type designation. This is a shortcut that enables to create |
|
219 |
* a new instance that differs only slightly from <i>this</i> type designation by |
|
220 |
* modifying only some of the attributes.<BR> |
|
221 |
* CAUTION: the typifiedNames set is not cloned but empty after cloning as the typified |
|
222 |
* names is considered to be the not owning part of a bidirectional relationship. |
|
223 |
* This may be changed in future. |
|
224 |
* |
|
225 |
* @throws CloneNotSupportedException |
|
226 |
* |
|
227 |
* @see eu.etaxonomy.cdm.model.common.ReferencedEntityBase#clone() |
|
228 |
* @see java.lang.Object#clone() |
|
229 |
*/ |
|
230 |
@Override |
|
231 |
public Object clone() throws CloneNotSupportedException { |
|
232 |
TypeDesignationBase result = (TypeDesignationBase)super.clone(); |
|
233 |
|
|
234 |
result.typifiedNames = new HashSet<TaxonNameBase>(); |
|
235 |
// for (TaxonNameBase taxonNameBase : getTypifiedNames()){ |
|
236 |
// result.typifiedNames.add(taxonNameBase); |
|
237 |
// } |
|
238 |
|
|
239 |
|
|
240 |
//no changes to: notDesignated, typeStatus, homotypicalGroup |
|
241 |
return result; |
|
242 |
} |
|
243 |
} |
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