/**
* Copyright (C) 2007 EDIT
-* European Distributed Institute of Taxonomy
+* European Distributed Institute of Taxonomy
* http://www.e-taxonomy.eu
-*
+*
* The contents of this file are subject to the Mozilla Public License Version 1.1
* See LICENSE.TXT at the top of this package for the full license terms.
*/
import java.lang.reflect.Method;
import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
import java.util.Set;
+import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.Inheritance;
import javax.persistence.InheritanceType;
+import javax.persistence.JoinTable;
import javax.persistence.ManyToMany;
import javax.persistence.ManyToOne;
import javax.persistence.OneToMany;
import javax.persistence.Transient;
+import javax.validation.Valid;
+import javax.validation.constraints.NotNull;
+import javax.validation.constraints.Size;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAnyElement;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlElement;
import javax.xml.bind.annotation.XmlElementWrapper;
import javax.xml.bind.annotation.XmlIDREF;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlSchemaType;
-import javax.xml.bind.annotation.XmlTransient;
import javax.xml.bind.annotation.XmlType;
import org.apache.log4j.Logger;
import org.hibernate.annotations.CascadeType;
import org.hibernate.annotations.Index;
import org.hibernate.annotations.Table;
-import org.hibernate.annotations.Target;
+import org.hibernate.envers.Audited;
+import org.hibernate.search.annotations.Field;
+import org.hibernate.search.annotations.IndexedEmbedded;
+import org.hibernate.validator.constraints.NotEmpty;
+import org.springframework.util.ReflectionUtils;
import eu.etaxonomy.cdm.model.common.IParsable;
import eu.etaxonomy.cdm.model.common.IReferencedEntity;
import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
import eu.etaxonomy.cdm.model.occurrence.Specimen;
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
-import eu.etaxonomy.cdm.model.reference.ReferenceBase;
-import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;
+import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.taxon.Synonym;
import eu.etaxonomy.cdm.model.taxon.Taxon;
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
+import eu.etaxonomy.cdm.strategy.cache.TaggedText;
+import eu.etaxonomy.cdm.strategy.cache.name.CacheUpdate;
import eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy;
+import eu.etaxonomy.cdm.strategy.match.IMatchable;
+import eu.etaxonomy.cdm.strategy.match.Match;
+import eu.etaxonomy.cdm.strategy.match.Match.ReplaceMode;
+import eu.etaxonomy.cdm.strategy.match.MatchMode;
+import eu.etaxonomy.cdm.strategy.merge.Merge;
+import eu.etaxonomy.cdm.strategy.merge.MergeMode;
+import eu.etaxonomy.cdm.strategy.parser.ParserProblem;
+import eu.etaxonomy.cdm.validation.Level2;
+import eu.etaxonomy.cdm.validation.annotation.NullOrNotEmpty;
/**
* The upmost (abstract) class for scientific taxon names regardless of any
* particular {@link NomenclaturalCode nomenclature code}. The scientific taxon name does not depend
* on the use made of it in a publication or a treatment
- * ({@link taxon.TaxonBase taxon concept respectively potential taxon})
- * as an {@link taxon.Taxon "accepted" respectively "correct" (taxon) name}
- * or as a {@link taxon.Synonym synonym}.
+ * ({@link eu.etaxonomy.cdm.model.taxon.TaxonBase taxon concept respectively potential taxon})
+ * as an {@link eu.etaxonomy.cdm.model.taxon.Taxon "accepted" respectively "correct" (taxon) name}
+ * or as a {@link eu.etaxonomy.cdm.model.taxon.Synonym synonym}.
* <P>
* This class corresponds partially to: <ul>
* <li> TaxonName according to the TDWG ontology
* <li> ScientificName and CanonicalName according to the TCS
* <li> ScientificName according to the ABCD schema
* </ul>
- *
+ *
* @author m.doering
* @version 1.0
* @created 08-Nov-2007 13:06:57
"nomenclaturalMicroReference",
"nomenclaturalReference",
"rank",
+ "fullTitleCache",
+ "protectedFullTitleCache",
"homotypicalGroup",
- "nameTypeDesignations",
- "specimenTypeDesignations",
+ "typeDesignations",
"relationsFromThisName",
"relationsToThisName",
"status",
- "descriptions"
-// "taxonBases"
+ "descriptions",
+ "taxonBases"
})
@XmlRootElement(name = "TaxonNameBase")
@Entity
+@Audited
@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
-@Table(appliesTo="TaxonNameBase", indexes = { @Index(name = "taxonNameBaseTitleCacheIndex", columnNames = { "persistentTitleCache" }) })
-public abstract class TaxonNameBase<T extends TaxonNameBase, S extends INameCacheStrategy> extends IdentifiableEntity<TaxonNameBase> implements IReferencedEntity, IParsable, IRelated {
+@Table(appliesTo="TaxonNameBase", indexes = { @Index(name = "taxonNameBaseTitleCacheIndex", columnNames = { "titleCache" }), @Index(name = "taxonNameBaseNameCacheIndex", columnNames = { "nameCache" }) })
+public abstract class TaxonNameBase<T extends TaxonNameBase<?,?>, S extends INameCacheStrategy> extends IdentifiableEntity<S> implements IReferencedEntity, IParsable, IRelated, IMatchable, Cloneable {
+ private static final long serialVersionUID = -4530368639601532116L;
+ private static final Logger logger = Logger.getLogger(TaxonNameBase.class);
- static Logger logger = Logger.getLogger(TaxonNameBase.class);
+ @XmlElement(name = "FullTitleCache")
+ @Column(length=330, name="fullTitleCache")
+ @Match(value=MatchMode.CACHE, cacheReplaceMode=ReplaceMode.ALL)
+ @CacheUpdate(noUpdate ="titleCache")
+ @NotEmpty(groups = Level2.class)
+ @Size(max = 330)
+ protected String fullTitleCache;
- private static Method methodDescriptionSetTaxonName;
+ //if true titleCache will not be automatically generated/updated
+ @XmlElement(name = "ProtectedFullTitleCache")
+ @CacheUpdate(value ="fullTitleCache", noUpdate ="titleCache")
+ private boolean protectedFullTitleCache;
@XmlElementWrapper(name = "Descriptions")
@XmlElement(name = "Description")
- private Set<TaxonNameDescription> descriptions = new HashSet<TaxonNameDescription>();
-
+ @OneToMany(mappedBy="taxonName", fetch= FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE, CascadeType.DELETE_ORPHAN})
+ @NotNull
+ private Set<TaxonNameDescription> descriptions = new HashSet<TaxonNameDescription>();
+
@XmlElement(name = "AppendedPhrase")
- private String appendedPhrase;
-
+ @Field(index= org.hibernate.search.annotations.Index.TOKENIZED)
+ @CacheUpdate(value ="nameCache")
+ @NullOrNotEmpty
+ @Size(max = 255)
+ private String appendedPhrase;
+
@XmlElement(name = "NomenclaturalMicroReference")
- private String nomenclaturalMicroReference;
-
+ @Field(index= org.hibernate.search.annotations.Index.TOKENIZED)
+ @CacheUpdate(noUpdate ="titleCache")
+ @NullOrNotEmpty
+ @Size(max = 255)
+ private String nomenclaturalMicroReference;
+
@XmlAttribute
- private boolean hasProblem = false;
-
- @XmlElementWrapper(name = "NameTypeDesignations")
- @XmlElement(name = "NameTypeDesignation")
- protected Set<NameTypeDesignation> nameTypeDesignations = new HashSet<NameTypeDesignation>();
-
- @XmlElementWrapper(name = "SpecimenTypeDesignations")
- @XmlElement(name = "SpecimenTypeDesignation")
- private Set<SpecimenTypeDesignation> specimenTypeDesignations = new HashSet<SpecimenTypeDesignation>();
-
- // List homotypical groups here in TaxonomicNames or separately?
- // FIXME: Stack overflow if listed here.
+ @CacheUpdate(noUpdate ={"titleCache","fullTitleCache"})
+ private int parsingProblem = 0;
+
+ @XmlAttribute
+ @CacheUpdate(noUpdate ={"titleCache","fullTitleCache"})
+ private int problemStarts = -1;
+
+ @XmlAttribute
+ @CacheUpdate(noUpdate ={"titleCache","fullTitleCache"})
+ private int problemEnds = -1;
+
+ @XmlElementWrapper(name = "TypeDesignations")
+ @XmlElement(name = "TypeDesignation")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @ManyToMany(fetch = FetchType.LAZY)
+ @JoinTable(
+ name="TaxonNameBase_TypeDesignationBase",
+ joinColumns=@javax.persistence.JoinColumn(name="TaxonNameBase_id"),
+ inverseJoinColumns=@javax.persistence.JoinColumn(name="typedesignations_id")
+ )
+ @Cascade({CascadeType.SAVE_UPDATE})
+ @NotNull
+ private Set<TypeDesignationBase> typeDesignations = new HashSet<TypeDesignationBase>();
+
@XmlElement(name = "HomotypicalGroup")
@XmlIDREF
@XmlSchemaType(name = "IDREF")
- private HomotypicalGroup homotypicalGroup = new HomotypicalGroup();
+ @ManyToOne(fetch = FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE})
+ @Match(MatchMode.IGNORE)
+ @CacheUpdate(noUpdate ="titleCache")
+ @NotNull
+ private HomotypicalGroup homotypicalGroup;
@XmlElementWrapper(name = "RelationsFromThisName")
@XmlElement(name = "RelationFromThisName")
- @XmlIDREF
- private Set<NameRelationship> relationsFromThisName = new HashSet<NameRelationship>();
+ @OneToMany(mappedBy="relatedFrom", fetch= FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE_ORPHAN})
+ @Merge(MergeMode.RELATION)
+ @NotNull
+ @Valid
+ private Set<NameRelationship> relationsFromThisName = new HashSet<NameRelationship>();
@XmlElementWrapper(name = "RelationsToThisName")
@XmlElement(name = "RelationToThisName")
@XmlIDREF
- private Set<NameRelationship> relationsToThisName = new HashSet<NameRelationship>();
+ @XmlSchemaType(name = "IDREF")
+ @OneToMany(mappedBy="relatedTo", fetch= FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE , CascadeType.DELETE_ORPHAN })
+ @Merge(MergeMode.RELATION)
+ @NotNull
+ @Valid
+ private Set<NameRelationship> relationsToThisName = new HashSet<NameRelationship>();
- @XmlElementWrapper(name = "Statuses")
- @XmlElement(name = "Status")
- @XmlIDREF
- private Set<NomenclaturalStatus> status = new HashSet<NomenclaturalStatus>();
+ @XmlElementWrapper(name = "NomenclaturalStatuses")
+ @XmlElement(name = "NomenclaturalStatus")
+ @OneToMany(fetch= FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE,CascadeType.DELETE,CascadeType.DELETE_ORPHAN})
+ @NotNull
+ @IndexedEmbedded(depth=3)
+ private Set<NomenclaturalStatus> status = new HashSet<NomenclaturalStatus>();
- @XmlTransient
- //@XmlElementWrapper(name = "TaxonBases")
- //@XmlElement(name = "TaxonBase")
- private Set<TaxonBase> taxonBases = new HashSet<TaxonBase>();
+ @XmlElementWrapper(name = "TaxonBases")
+ @XmlElement(name = "TaxonBase")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @OneToMany(mappedBy="name", fetch= FetchType.LAZY)
+ @NotNull
+ private Set<TaxonBase> taxonBases = new HashSet<TaxonBase>();
@XmlElement(name = "Rank")
- @XmlIDREF
- @XmlSchemaType(name = "IDREF")
- private Rank rank;
-
-// FIXME: This must be an IDREF to the corresponding nomenclatural reference.
- @XmlAnyElement
- private INomenclaturalReference nomenclaturalReference;
-
- static Method methodTaxonBaseSetName;
-
-// ************* CONSTRUCTORS *************/
- /**
- * Class constructor: creates a new empty taxon name.
- *
- * @see #TaxonNameBase(Rank)
- * @see #TaxonNameBase(HomotypicalGroup)
- * @see #TaxonNameBase(Rank, HomotypicalGroup)
- */
- public TaxonNameBase() {
- this(null, null);
- }
- /**
- * Class constructor: creates a new taxon name
- * only containing its {@link common.Rank rank}.
- *
- * @param rank the rank to be assigned to <i>this</i> taxon name
- * @see #TaxonNameBase()
- * @see #TaxonNameBase(HomotypicalGroup)
- * @see #TaxonNameBase(Rank, HomotypicalGroup)
- */
- public TaxonNameBase(Rank rank) {
- this(rank, null);
- }
- /**
- * Class constructor: creates a new taxon name
- * only containing its {@link HomotypicalGroup homotypical group}.
- * The new taxon name will be also added to the set of taxon names
- * belonging to this homotypical group.
- *
- * @param homotypicalGroup the homotypical group to which <i>this</i> taxon name belongs
- * @see #TaxonNameBase()
- * @see #TaxonNameBase(Rank)
- * @see #TaxonNameBase(Rank, HomotypicalGroup)
- */
- public TaxonNameBase(HomotypicalGroup homotypicalGroup) {
- this(null, homotypicalGroup);
- }
- /**
- * Class constructor: creates a new taxon name
- * only containing its {@link common.Rank rank} and
- * its {@link HomotypicalGroup homotypical group}.
- * The new taxon name will be also added to the set of taxon names
- * belonging to this homotypical group.
- *
- * @param rank the rank to be assigned to <i>this</i> taxon name
- * @param homotypicalGroup the homotypical group to which <i>this</i> taxon name belongs
- * @see #TaxonNameBase()
- * @see #TaxonNameBase(Rank)
- * @see #TaxonNameBase(HomotypicalGroup)
- */
- public TaxonNameBase(Rank rank, HomotypicalGroup homotypicalGroup) {
- super();
- this.setRank(rank);
- if (homotypicalGroup == null){
- homotypicalGroup = new HomotypicalGroup();
- }
- homotypicalGroup.addTypifiedName(this);
- }
-
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @ManyToOne(fetch = FetchType.EAGER)
+ @CacheUpdate(value ="nameCache")
+ @NotNull
+ @IndexedEmbedded(depth=3)
+ private Rank rank;
+
+ @XmlElement(name = "NomenclaturalReference")
+ @XmlIDREF
+ @XmlSchemaType(name = "IDREF")
+ @ManyToOne(fetch = FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE})
+ @CacheUpdate(noUpdate ="titleCache")
+ @IndexedEmbedded
+ private Reference nomenclaturalReference;
+
+// ************* CONSTRUCTORS *************/
+ /**
+ * Class constructor: creates a new empty taxon name.
+ *
+ * @see #TaxonNameBase(Rank)
+ * @see #TaxonNameBase(HomotypicalGroup)
+ * @see #TaxonNameBase(Rank, HomotypicalGroup)
+ */
+ public TaxonNameBase() {
+ super();
+ }
+ /**
+ * Class constructor: creates a new taxon name
+ * only containing its {@link Rank rank}.
+ *
+ * @param rank the rank to be assigned to <i>this</i> taxon name
+ * @see #TaxonNameBase()
+ * @see #TaxonNameBase(HomotypicalGroup)
+ * @see #TaxonNameBase(Rank, HomotypicalGroup)
+ */
+ public TaxonNameBase(Rank rank) {
+ this(rank, null);
+ }
+ /**
+ * Class constructor: creates a new taxon name
+ * only containing its {@link HomotypicalGroup homotypical group}.
+ * The new taxon name will be also added to the set of taxon names
+ * belonging to this homotypical group.
+ *
+ * @param homotypicalGroup the homotypical group to which <i>this</i> taxon name belongs
+ * @see #TaxonNameBase()
+ * @see #TaxonNameBase(Rank)
+ * @see #TaxonNameBase(Rank, HomotypicalGroup)
+ */
+ public TaxonNameBase(HomotypicalGroup homotypicalGroup) {
+ this(null, homotypicalGroup);
+ }
+ /**
+ * Class constructor: creates a new taxon name
+ * only containing its {@link Rank rank} and
+ * its {@link HomotypicalGroup homotypical group}.
+ * The new taxon name will be also added to the set of taxon names
+ * belonging to this homotypical group.
+ *
+ * @param rank the rank to be assigned to <i>this</i> taxon name
+ * @param homotypicalGroup the homotypical group to which <i>this</i> taxon name belongs
+ * @see #TaxonNameBase()
+ * @see #TaxonNameBase(Rank)
+ * @see #TaxonNameBase(HomotypicalGroup)
+ */
+ public TaxonNameBase(Rank rank, HomotypicalGroup homotypicalGroup) {
+ super();
+ this.setRank(rank);
+ if (homotypicalGroup == null){
+ homotypicalGroup = new HomotypicalGroup();
+ }
+ homotypicalGroup.addTypifiedName(this);
+ }
+
+ abstract protected Map<String, java.lang.reflect.Field> getAllFields();
+
//********* METHODS **************************************/
- //@Index(name="TaxonNameBaseTitleCacheIndex")
-// public String getTitleCache(){
-// return super.getTitleCache();
-// }
-
- /**
- * Returns the boolean value "false" since the components of <i>this</i> taxon name
- * cannot follow the rules of a corresponding {@link NomenclaturalCode nomenclatural code}
- * which is not defined for this class. The nomenclature code depends on
- * the concrete name subclass ({@link BacterialName BacterialName},
- * {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName},
- * {@link ZoologicalName ZoologicalName} or {@link ViralName ViralName})
- * to which a taxon name belongs.
- *
- * @return false
- */
- @Transient
- public abstract boolean isCodeCompliant();
-
-
- /**
- * Returns the set of all {@link NameRelationship name relationships}
- * in which <i>this</i> taxon name is involved. A taxon name can be both source
- * in some name relationships or target in some others.
- *
- * @see #getRelationsToThisName()
- * @see #getRelationsFromThisName()
- * @see #addNameRelationship(NameRelationship)
- * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
- * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
- */
- @Transient
- public Set<NameRelationship> getNameRelations() {
- Set<NameRelationship> rels = new HashSet<NameRelationship>();
- rels.addAll(getRelationsFromThisName());
- rels.addAll(getRelationsToThisName());
- return rels;
- }
- /**
- * Creates a new {@link NameRelationship#NameRelationship(TaxonNameBase, TaxonNameBase, NameRelationshipType, String) name relationship} from <i>this</i> taxon name to another taxon name
- * and adds it both to the set of {@link #getRelationsFromThisName() relations from <i>this</i> taxon name} and
- * to the set of {@link #getRelationsToThisName() relations to the other taxon name}.
- *
- * @param toName the taxon name of the target for this new name relationship
- * @param type the type of this new name relationship
- * @param ruleConsidered the string which specifies the rule on which this name relationship is based
- * @see #getRelationsToThisName()
- * @see #getNameRelations()
- * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
- * @see #addNameRelationship(NameRelationship)
- */
- public void addRelationshipToName(TaxonNameBase toName, NameRelationshipType type, String ruleConsidered){
- NameRelationship rel = new NameRelationship(toName, this, type, ruleConsidered);
- }
- /**
- * Creates a new {@link NameRelationship#NameRelationship(TaxonNameBase, TaxonNameBase, NameRelationshipType, String) name relationship} from another taxon name to <i>this</i> taxon name
- * and adds it both to the set of {@link #getRelationsToThisName() relations to <i>this</i> taxon name} and
- * to the set of {@link #getRelationsFromThisName() relations from the other taxon name}.
- *
- * @param fromName the taxon name of the source for this new name relationship
- * @param type the type of this new name relationship
- * @param ruleConsidered the string which specifies the rule on which this name relationship is based
- * @see #getRelationsFromThisName()
- * @see #getNameRelations()
- * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
- * @see #addNameRelationship(NameRelationship)
- */
- public void addRelationshipFromName(TaxonNameBase fromName, NameRelationshipType type, String ruleConsidered){
- NameRelationship rel = new NameRelationship(this, fromName, type, ruleConsidered);
- }
- /**
- * Adds an existing {@link NameRelationship name relationship} either to the set of
- * {@link #getRelationsToThisName() relations to <i>this</i> taxon name} or to the set of
- * {@link #getRelationsFromThisName() relations from <i>this</i> taxon name}. If neither the
- * source nor the target of the name relationship match with <i>this</i> taxon name
- * no addition will be carried out.
- *
- * @param rel the name relationship to be added to one of <i>this</i> taxon name's name relationships sets
- * @see #getNameRelations()
- * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
- * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
- */
- protected void addNameRelationship(NameRelationship rel) {
- if (rel!=null && rel.getToName().equals(this)){
- this.relationsToThisName.add(rel);
- }else if(rel!=null && rel.getFromName().equals(this)){
- this.relationsFromThisName.add(rel);
- }else{
- //TODO: raise error???
- }
- }
- /**
- * Removes one {@link NameRelationship name relationship} from one of both sets of
- * {@link #getNameRelations() name relationships} in which <i>this</i> taxon name is involved.
- * The name relationship will also be removed from one of both sets belonging
- * to the second taxon name involved. Furthermore the fromName and toName
- * attributes of the name relationship object will be nullified.
- *
- * @param nameRelation the name relationship which should be deleted from one of both sets
- * @see #getNameRelations()
- */
- public void removeNameRelationship(NameRelationship nameRelation) {
- //TODO to be implemented?
- logger.warn("not yet fully implemented?");
- this.relationsToThisName.remove(nameRelation);
- this.relationsFromThisName.remove(nameRelation);
- }
-
-
- /**
- * Does exactly the same as the addNameRelationship method provided that
- * the given relationship is a name relationship.
- *
- * @param relation the relationship to be added to one of <i>this</i> taxon name's name relationships sets
- * @see #addNameRelationship(NameRelationship)
- * @see #getNameRelations()
- * @see NameRelationship
- * @see common.RelationshipBase
- */
- public void addRelationship(RelationshipBase relation) {
- if (relation instanceof NameRelationship){
- addNameRelationship((NameRelationship)relation);
- if (relation.getType() != null &&
- ( relation.getType().equals(NameRelationshipType.BASIONYM()) ||
- relation.getType().equals(NameRelationshipType.REPLACED_SYNONYM())
- )){
- TaxonNameBase fromName = ((NameRelationship)relation).getFromName();
- TaxonNameBase toName = ((NameRelationship)relation).getToName();
- fromName.getHomotypicalGroup().merge(toName.getHomotypicalGroup());
- }
- }else{
- logger.warn("Relationship not of type NameRelationship!");
- //TODO exception handling
- }
- }
-
-
- /**
- * Returns the set of all {@link NameRelationship name relationships}
- * in which <i>this</i> taxon name is involved as a source.
- *
- * @see #getNameRelations()
- * @see #getRelationsToThisName()
- * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
- */
- @OneToMany(mappedBy="relatedFrom", fetch= FetchType.LAZY)
- @Cascade({CascadeType.SAVE_UPDATE})
- public Set<NameRelationship> getRelationsFromThisName() {
- return relationsFromThisName;
- }
- private void setRelationsFromThisName(Set<NameRelationship> relationsFromThisName) {
- this.relationsFromThisName = relationsFromThisName;
- }
-
- /**
- * Returns the set of all {@link NameRelationship name relationships}
- * in which <i>this</i> taxon name is involved as a target.
- *
- * @see #getNameRelations()
- * @see #getRelationsFromThisName()
- * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
- */
- @OneToMany(mappedBy="relatedTo", fetch= FetchType.LAZY)
- @Cascade({CascadeType.SAVE_UPDATE})
- public Set<NameRelationship> getRelationsToThisName() {
- return relationsToThisName;
- }
- private void setRelationsToThisName(Set<NameRelationship> relationsToThisName) {
- this.relationsToThisName = relationsToThisName;
- }
-
-
- /**
- * Returns the set of {@link NomenclaturalStatus nomenclatural status} assigned
- * to <i>this</i> taxon name according to its corresponding nomenclature code.
- * This includes the {@link NomenclaturalStatusType type} of the nomenclatural status
- * and the nomenclatural code rule considered.
- *
- * @see NomenclaturalStatus
- * @see NomenclaturalStatusType
- */
- @OneToMany(fetch= FetchType.LAZY)
- @Cascade({CascadeType.SAVE_UPDATE})
- public Set<NomenclaturalStatus> getStatus() {
- return status;
- }
- /**
- * @see #getStatus()
- */
- protected void setStatus(Set<NomenclaturalStatus> nomStatus) {
- this.status = nomStatus;
- }
- /**
- * Adds a new {@link NomenclaturalStatus nomenclatural status}
- * to <i>this</i> taxon name's set of nomenclatural status.
- *
- * @param nomStatus the nomenclatural status to be added
- * @see #getStatus()
- */
- public void addStatus(NomenclaturalStatus nomStatus) {
- this.status.add(nomStatus);
- }
- /**
- * Removes one element from the set of nomenclatural status of <i>this</i> taxon name.
- * Type and ruleConsidered attributes of the nomenclatural status object
- * will be nullified.
- *
- * @param nomStatus the nomenclatural status of <i>this</i> taxon name which should be deleted
- * @see #getStatus()
- */
- public void removeStatus(NomenclaturalStatus nomStatus) {
- //TODO to be implemented?
- logger.warn("not yet fully implemented?");
- this.status.remove(nomStatus);
- }
-
-
- /**
- * Indicates whether <i>this</i> taxon name is a {@link NameRelationshipType.BASIONYM() basionym}
- * or a {@link NameRelationshipType.REPLACED_SYNONYM() replaced synonym}
- * of any other taxon name. Returns "true", if a basionym or a replaced
- * synonym relationship from <i>this</i> taxon name to another taxon name exists,
- * false otherwise (also in case <i>this</i> taxon name is the only one in the
- * homotypical group).
- */
- @Transient
- public boolean isOriginalCombination(){
- Set<NameRelationship> relationsFromThisName = this.getRelationsFromThisName();
- for (NameRelationship relation : relationsFromThisName) {
- if (relation.getType().equals(NameRelationshipType.BASIONYM()) ||
- relation.getType().equals(NameRelationshipType.REPLACED_SYNONYM())) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Returns the taxon name which is the {@link NameRelationshipType.BASIONYM() basionym} of <i>this</i> taxon name.
- * The basionym of a taxon name is its epithet-bringing synonym.
- * For instance Pinus abies L. was published by Linnaeus and the botanist
- * Karsten transferred later <i>this</i> taxon to the genus Picea. Therefore,
- * Pinus abies L. is the basionym of the new combination Picea abies (L.) H. Karst.
- */
- @Transient
- public T getBasionym(){
- //TODO: pick the right name relationships...
- logger.warn("get Basionym not yet implemented");
- return null;
- }
- /**
- * Assigns another taxon name as {@link NameRelationshipType.BASIONYM() basionym} of <i>this</i> taxon name.
- * The basionym relationship will be added to <i>this</i> taxon name
- * and to the basionym. The basionym cannot have itself a basionym.
- * The homotypical group of <i>this</i> taxon name will be changed the basionyms homotypical group.
- * @see #getBasionym()
- * @see #addBasionym(TaxonNameBase, String)
- */
- public void addBasionym(T basionym){
- addBasionym(basionym, null);
- }
- /**
- * Assigns another taxon name as {@link NameRelationshipType.BASIONYM() basionym} of <i>this</i> taxon name
- * and keeps the nomenclatural rule considered for it. The basionym
- * relationship will be added to <i>this</i> taxon name and to the basionym.
- * The basionym cannot have itself as a basionym.
- * The homotypical group of <i>this</i> taxon name will be changed the basionyms homotypical group.
- * @see #getBasionym()
- * @see #setBasionym(TaxonNameBase)
- */
- public void addBasionym(T basionym, String ruleConsidered){
- if (basionym != null){
- basionym.addRelationshipToName(this, NameRelationshipType.BASIONYM(), ruleConsidered);
- }
- }
-
- public void removeBasionym(){
- //TODO implement
- logger.warn("not yet implemented");
- }
-
-
-
- @Transient
- public abstract S getCacheStrategy();
- public abstract void setCacheStrategy(S cacheStrategy);
-
- /**
- * Returns the taxonomic {@link Rank rank} of <i>this</i> taxon name.
- *
- * @see Rank
- */
- @ManyToOne
- //@Cascade({CascadeType.SAVE_UPDATE})
- public Rank getRank(){
- return this.rank;
- }
- /**
- * @see #getRank()
- */
- public void setRank(Rank rank){
- this.rank = rank;
- }
-
- /**
- * Returns the {@link reference.INomenclaturalReference nomenclatural reference} of <i>this</i> taxon name.
- * The nomenclatural reference is here meant to be the one publication
- * <i>this</i> taxon name was originally published in while fulfilling the formal
- * requirements as specified by the corresponding {@link NomenclaturalCode nomenclatural codes}.
- *
- * @see reference.INomenclaturalReference
- * @see reference.ReferenceBase
- */
- @ManyToOne
- @Cascade({CascadeType.SAVE_UPDATE})
- @Target(ReferenceBase.class)
- public INomenclaturalReference getNomenclaturalReference(){
- return this.nomenclaturalReference;
- }
- /**
- * Assigns a nomenclatural {@link reference.INomenclaturalReference nomenclatural reference} to <i>this</i> taxon name.
- * The corresponding {@link reference.ReferenceBase.isNomenclaturallyRelevant nomenclaturally relevant flag} will be set to true
- * as it is obviously used for nomenclatural purposes.
- *
- * @see #getNomenclaturalReference()
- */
- public void setNomenclaturalReference(INomenclaturalReference nomenclaturalReference){
- this.nomenclaturalReference = nomenclaturalReference;
- }
-
- /**
- * Returns the appended phrase string assigned to <i>this</i> taxon name.
- * The appended phrase is a non-atomised addition to a name. It is
- * not ruled by a nomenclatural code.
- */
- public String getAppendedPhrase(){
- return this.appendedPhrase;
- }
- /**
- * @see #getAppendedPhrase()
- */
- public void setAppendedPhrase(String appendedPhrase){
- this.appendedPhrase = appendedPhrase;
- }
-
- /**
- * Returns the details string of the nomenclatural reference assigned
- * to <i>this</i> taxon name. The details describe the exact localisation within
- * the publication used as nomenclature reference. These are mostly
- * (implicitly) pages but can also be figures or tables or any other
- * element of a publication. A nomenclatural micro reference (details)
- * requires the existence of a nomenclatural reference.
- */
- //Details of the nomenclatural reference (protologue).
- public String getNomenclaturalMicroReference(){
- return this.nomenclaturalMicroReference;
- }
- /**
- * @see #getNomenclaturalMicroReference()
- */
- public void setNomenclaturalMicroReference(String nomenclaturalMicroReference){
- this.nomenclaturalMicroReference = nomenclaturalMicroReference;
- }
-
- /**
- * Returns the boolean value of the flag indicating whether the used {@link eu.etaxonomy.cdm.strategy.parser.INonViralNameParser parser}
- * method was able to parse the taxon name string successfully (false)
- * or not (true). The parser itself may also depend on the {@link NomenclaturalCode nomenclatural code}
- * governing the construction of <i>this</i> taxon name.
- *
- * @return the boolean value of the hasProblem flag
- * @see #getNameCache()
- */
- public boolean getHasProblem(){
- return this.hasProblem;
- }
- /**
- * @see #getHasProblem()
- */
- public void setHasProblem(boolean hasProblem){
- this.hasProblem = hasProblem;
- }
- /**
- * Returns exactly the same boolean value as the {@link #getHasProblem() getHasProblem} method.
- *
- * @see #getHasProblem()
- */
- public boolean hasProblem(){
- return getHasProblem();
- }
-
-
- /**
- * Returns the set of {@link NameTypeDesignation name type designations} assigned
- * to <i>this</i> taxon name the rank of which must be above "species".
- * The name type designations include all the taxon names used to typify
- * this name and eventually the rejected or conserved status
- * of these designations.
- *
- * @see NameTypeDesignation
- * @see SpecimenTypeDesignation
- */
- @OneToMany
- //TODO @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE_ORPHAN})
- @Cascade(CascadeType.SAVE_UPDATE)
- public Set<NameTypeDesignation> getNameTypeDesignations() {
- return nameTypeDesignations;
- }
- /**
- * @see #getNameTypeDesignations()
- */
- protected void setNameTypeDesignations(Set<NameTypeDesignation> nameTypeDesignations) {
- this.nameTypeDesignations = nameTypeDesignations;
- }
- public void addNameTypeDesignation(NameTypeDesignation nameTypeDesignation) {
- if (nameTypeDesignation != null){
- if (nameTypeDesignation.getTypifiedName() != null){
- nameTypeDesignation.getTypifiedName().getNameTypeDesignations().remove(nameTypeDesignation);
- }
- nameTypeDesignation.setTypifiedName(this);
- this.nameTypeDesignations.add(nameTypeDesignation);
- }
- }
-
-
- /**
- * Creates and adds a new {@link NameTypeDesignation name type designation}
- * to <i>this</i> taxon name's set of name type designations.
- *
- * @param typeSpecies the taxon name to be used as type of <i>this</i> taxon name
- * @param citation the reference for this new designation
- * @param citationMicroReference the string with the details (generally pages) within the reference
- * @param originalNameString the taxon name string used in the reference to assert this designation
- * @param isRejectedType the boolean status for rejected
- * @param isConservedType the boolean status for conserved
- * @param isLectoType the boolean status for isLectotype
- * @param lectoCitation the reference for the lectotype
- * @param lectoMicroCitation the String for the micro citation of a lectotype
- * @see #getNameTypeDesignations()
- * @see #addTypeDesignation(Specimen, TypeDesignationStatus, ReferenceBase, String, String)
- */
- public void addNameTypeDesignation(TaxonNameBase typeSpecies, ReferenceBase citation, String citationMicroReference, String originalNameString, boolean isRejectedType, boolean isConservedType, boolean isLectoType, ReferenceBase lectoCitation, String lectoMicroCitation, boolean isNotDesignated) {
- NameTypeDesignation td = new NameTypeDesignation(this, typeSpecies, citation, citationMicroReference, originalNameString, isRejectedType, isConservedType, isNotDesignated);
- }
-
- /**
- * Removes one element from the set of {@link NameTypeDesignation name type designations} of <i>this</i> taxon name.
- * The name type designation itself will be nullified.
- *
- * @param typeDesignation the name type designation of <i>this</i> taxon name which should be deleted
- * @see #getNameTypeDesignations()
- * @see #removeTypeDesignation(SpecimenTypeDesignation)
- */
- public void removeNameTypeDesignation(NameTypeDesignation typeDesignation) {
- //TODO
- logger.warn("not yet fully implemented: nullify the name type designation itself?");
- this.nameTypeDesignations.remove(typeDesignation);
- }
-
- /**
- * Returns the set of {@link SpecimenTypeDesignation specimen type designations}
- * that typify <i>this</i> taxon name.
- */
- @ManyToMany
- @Cascade(CascadeType.SAVE_UPDATE)
- public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations() {
- return specimenTypeDesignations;
- }
- /**
- * @see #getSpecimenTypeDesignations()
- */
- protected void setSpecimenTypeDesignations(Set<SpecimenTypeDesignation> specimenTypeDesignations) {
- this.specimenTypeDesignations = specimenTypeDesignations;
- }
-
- /**
- * Returns the set of {@link SpecimenTypeDesignation specimen type designations} assigned
- * indirectly to <i>this</i> taxon name through its {@link HomotypicalGroup homotypical group}.
- * The rank of <i>this</i> taxon name is generally "species" or below.
- * The specimen type designations include all the specimens on which
- * the typification of this name is based (and which are common to all
- * taxon names belonging to the homotypical group) and eventually
- * the status of these designations.
- *
- * @see SpecimenTypeDesignation
- * @see NameTypeDesignation
- */
- @Transient
- public Set<SpecimenTypeDesignation> getSpecimenTypeDesignationsOfHomotypicalGroup() {
- return this.getHomotypicalGroup().getTypeDesignations();
- }
-
- /**
- * Adds a new {@link SpecimenTypeDesignation specimen type designation}
- * (using its attributes as parameters) to the set of specimen type designations assigned to the
- * {@link HomotypicalGroup homotypical group} to which <i>this</i> taxon name belongs.
- *
- * @param typeSpecimen the specimen to be used as a type for <i>this</i> taxon name's homotypical group
- * @param status the specimen type designation status
- * @param citation the reference for this new specimen type designation
- * @param citationMicroReference the string with the details (generally pages) within the reference
- * @param originalNameString the taxon name used in the reference to assert this designation
- * @see HomotypicalGroup#getTypeDesignations()
- * @see #addTypeDesignation(TaxonNameBase, ReferenceBase, String, String, boolean, boolean)
- * @see TypeDesignationStatus
- */
- public void addSpecimenTypeDesignation(Specimen typeSpecimen, TypeDesignationStatus status, ReferenceBase citation, String citationMicroReference, String originalNameString, boolean addToAllNames) {
- SpecimenTypeDesignation specimenTypeDesignation =
- SpecimenTypeDesignation.NewInstance(typeSpecimen, status, citation, citationMicroReference, originalNameString);
- this.getHomotypicalGroup().addTypeDesignation(specimenTypeDesignation, addToAllNames);
- }
-
- //only to be used for xxx
- /**
- * Adds a new {@link SpecimenTypeDesignation specimen type designation}
- * to the set of specimen type designations assigned to the
- * {@link HomotypicalGroup homotypical group} to which <i>this</i> taxon name belongs.
- *
- * @param specimenTypeDesignation the specimen type designation to be added for <i>this</i> taxon name's homotypical group
- * @see #addSpecimenTypeDesignation(Specimen, TypeDesignationStatus, ReferenceBase, String, String, boolean)
- * @see HomotypicalGroup#getTypeDesignations()
- * @see #addTypeDesignation(TaxonNameBase, ReferenceBase, String, String, boolean, boolean)
- */
- protected void addSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation) {
- this.specimenTypeDesignations.add(specimenTypeDesignation);
- }
-
- //only to be used for xxx
- /**
- * Removes one element from the set of {@link SpecimenTypeDesignation specimen type designations} assigned to the
- * {@link HomotypicalGroup homotypical group} to which <i>this</i> taxon name belongs.
- *
- * @param SpecimenTypeDesignation the specimen type designation which should be deleted
- * @see HomotypicalGroup#getTypeDesignations()
- * @see #removeTypeDesignation(SpecimenTypeDesignation)
- * @see #removeNameTypeDesignation(NameTypeDesignation)
- */
- protected void removeSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation) {
- this.specimenTypeDesignations.remove(specimenTypeDesignation);
- }
-
- /**
- * Removes one element from the set of {@link SpecimenTypeDesignation specimen type designations} assigned to the
- * {@link HomotypicalGroup homotypical group} to which <i>this</i> taxon name belongs.
- * The specimen type designation itself will be nullified.
- *
- * @param typeDesignation the specimen type designation which should be deleted
- * @see HomotypicalGroup#getTypeDesignations()
- * @see #removeSpecimenTypeDesignation(SpecimenTypeDesignation)
- * @see #removeNameTypeDesignation(NameTypeDesignation)
- */
- public void removeTypeDesignation(SpecimenTypeDesignation typeDesignation) {
- logger.warn("not yet fully implemented: nullify the specimen type designation itself?");
- this.homotypicalGroup.removeTypeDesignation(typeDesignation);
- }
-
- /**
- * Returns the {@link HomotypicalGroup homotypical group} to which
- * <i>this</i> taxon name belongs. A homotypical group represents all taxon names
- * that share the same type specimens.
- *
- * @see HomotypicalGroup
- */
- @ManyToOne
- @Cascade({CascadeType.SAVE_UPDATE})
- public HomotypicalGroup getHomotypicalGroup() {
- return homotypicalGroup;
- }
- @Deprecated //only for bidirectional and persistence use
- protected void setHomotypicalGroup(HomotypicalGroup newHomotypicalGroup) {
- this.homotypicalGroup = newHomotypicalGroup;
- }
-
- /**
- * @see #getNomenclaturalReference()
- */
- @Transient
- public StrictReferenceBase getCitation(){
- //TODO What is the purpose of this method differing from the getNomenclaturalReference method?
- logger.warn("getCitation not yet implemented");
- return null;
- }
-
- /**
- * Returns the complete string containing the
- * {@link reference.INomenclaturalReference#getNomenclaturalCitation() nomenclatural reference citation}
- * (including {@link #getNomenclaturalMicroReference() details}) assigned to <i>this</i> taxon name.
- *
- * @return the string containing the nomenclatural reference of <i>this</i> taxon name
- * @see reference.INomenclaturalReference#getNomenclaturalCitation()
- * @see #getNomenclaturalReference()
- * @see #getNomenclaturalMicroReference()
- */
- @Transient
- public String getCitationString(){
- logger.warn("getCitationString not yet implemented");
- return null;
- }
-
- @Transient
- public String[] getProblems(){
- logger.warn("getProblems not yet implemented");
- return null;
- }
-
- /**
- * Returns the string containing the publication date (generally only year)
- * of the nomenclatural reference for <i>this</i> taxon name, null if there is
- * no nomenclatural reference.
- *
- * @return the string containing the publication date of <i>this</i> taxon name
- * @see reference.INomenclaturalReference#getYear()
- */
- @Transient
- public String getReferenceYear(){
- if (this.getNomenclaturalReference() != null ){
- return this.getNomenclaturalReference().getYear();
- }else{
- return null;
- }
- }
-
- /**
- * Returns the set of {@link taxon.TaxonBase taxon bases} that refer to <i>this</i> taxon name.
- * In this context a taxon base means the use of a taxon name by a reference
- * either as a taxon ("accepted/correct" name) or as a (junior) synonym.
- * A taxon name can be used by several distinct references but only once
- * within a taxonomic treatment (identified by one reference).
- *
- * @see taxon.TaxonBase
- * @see #getTaxa()
- * @see #getSynonyms()
- */
- @OneToMany(mappedBy="name", fetch= FetchType.LAZY)
- public Set<TaxonBase> getTaxonBases() {
- return this.taxonBases;
- }
- /**
- * @see #getTaxonBases()
- */
- protected void setTaxonBases(Set<TaxonBase> taxonBases) {
- if (taxonBases == null){
- taxonBases = new HashSet<TaxonBase>();
- }else{
- this.taxonBases = taxonBases;
- }
- }
- /**
- * Adds a new {@link taxon.TaxonBase taxon base}
- * to the set of taxon bases using <i>this</i> taxon name.
- *
- * @param taxonBase the taxon base to be added
- * @see #getTaxonBases()
- * @see #removeTaxonBase(TaxonBase)
- */
- //TODO protected
- public void addTaxonBase(TaxonBase taxonBase){
- taxonBases.add(taxonBase);
- initMethods();
- invokeSetMethod(methodTaxonBaseSetName, taxonBase);
- }
- /**
- * Removes one element from the set of {@link taxon.TaxonBase taxon bases} that refer to <i>this</i> taxon name.
- *
- * @param taxonBase the taxon base which should be removed from the corresponding set
- * @see #addTaxonBase(TaxonBase)
- */
- public void removeTaxonBase(TaxonBase taxonBase){
- taxonBases.remove(taxonBase);
- initMethods();
- invokeSetMethodWithNull(methodTaxonBaseSetName, taxonBase);
- }
-
- private void initMethods(){
- if (methodTaxonBaseSetName == null){
- try {
- methodTaxonBaseSetName = TaxonBase.class.getDeclaredMethod("setName", TaxonNameBase.class);
- methodTaxonBaseSetName.setAccessible(true);
- } catch (Exception e) {
- e.printStackTrace();
- //TODO handle exception
- }
- }
- if (methodDescriptionSetTaxonName == null){
- try {
- methodDescriptionSetTaxonName = TaxonNameDescription.class.getDeclaredMethod("setTaxonName", TaxonNameBase.class);
- methodDescriptionSetTaxonName.setAccessible(true);
- } catch (Exception e) {
- e.printStackTrace();
- //TODO handle exception
- }
- }
- }
-
-
-
- /**
- * Returns the set of {@link taxon.Taxon taxa} ("accepted/correct" names according to any
- * reference) that are based on <i>this</i> taxon name. This set is a subset of
- * the set returned by getTaxonBases().
- *
- * @see taxon.Taxon
- * @see #getTaxonBases()
- * @see #getSynonyms()
- */
- @Transient
- public Set<Taxon> getTaxa(){
- Set<Taxon> result = new HashSet<Taxon>();
- for (TaxonBase taxonBase : this.taxonBases){
- if (taxonBase instanceof Taxon){
- result.add((Taxon)taxonBase);
- }
- }
- return result;
- }
-
- /**
- * Returns the set of {@link taxon.Synonym (junior) synonyms} (according to any
- * reference) that are based on <i>this</i> taxon name. This set is a subset of
- * the set returned by getTaxonBases().
- *
- * @see taxon.Synonym
- * @see #getTaxonBases()
- * @see #getTaxa()
- */
- @Transient
- public Set<Synonym> getSynonyms() {
- Set<Synonym> result = new HashSet<Synonym>();
- for (TaxonBase taxonBase : this.taxonBases){
- if (taxonBase instanceof Synonym){
- result.add((Synonym)taxonBase);
- }
- }
- return result;
- }
-
-
-// *********** DESCRIPTIONS *************************************
-
- /**
- * Returns the set of {@link description.TaxonNameDescription taxon name descriptions} assigned
- * to <i>this</i> taxon name. A taxon name description is a piece of information
- * concerning the taxon name like for instance the content of its first
- * publication (protolog) or a picture of this publication.
- *
- * @see #addDescription(TaxonNameDescription)
- * @see #removeDescription(TaxonNameDescription)
- * @see description.TaxonNameDescription
- */
- @OneToMany(mappedBy="taxonName", fetch= FetchType.LAZY)
- @Cascade({CascadeType.SAVE_UPDATE})
- public Set<TaxonNameDescription> getDescriptions() {
- return descriptions;
- }
- /**
- * @see #getDescriptions()
- */
- protected void setDescriptions(Set<TaxonNameDescription> descriptions) {
- this.descriptions = descriptions;
- }
- /**
- * Adds a new {@link description.TaxonNameDescription taxon name description}
- * to the set of taxon name descriptions assigned to <i>this</i> taxon name. The
- * content of the {@link description.TaxonNameDescription#getTaxonName() taxonName attribute} of the
- * taxon name description itself will be replaced with <i>this</i> taxon name.
- *
- * @param description the taxon name description to be added
- * @see #getDescriptions()
- * @see #removeDescription(TaxonNameDescription)
- */
- public void addDescription(TaxonNameDescription description) {
- initMethods();
- this.invokeSetMethod(methodDescriptionSetTaxonName, description);
- descriptions.add(description);
- }
- /**
- * Removes one element from the set of {@link description.TaxonNameDescription taxon name descriptions} assigned
- * to <i>this</i> taxon name. The content of the {@link description.TaxonNameDescription#getTaxonName() taxonName attribute}
- * of the description itself will be set to "null".
- *
- * @param description the taxon name description which should be removed
- * @see #getDescriptions()
- * @see #addDescription(TaxonNameDescription)
- * @see description.TaxonNameDescription#getTaxonName()
- */
- public void removeDescription(TaxonNameDescription description) {
- initMethods();
- this.invokeSetMethod(methodDescriptionSetTaxonName, null);
- descriptions.remove(description);
- }
-
-
-
-
-
-
-// ***********
- /**
- * Returns the boolean value indicating whether a given taxon name belongs
- * to the same {@link HomotypicalGroup homotypical group} as <i>this</i> taxon name (true)
- * or not (false). Returns "true" only if the homotypical groups of both
- * taxon names exist and if they are identical.
- *
- * @param homoTypicName the taxon name the homotypical group of which is to be checked
- * @return the boolean value of the check
- * @see HomotypicalGroup
- */
- public boolean isHomotypic(TaxonNameBase homoTypicName) {
- if (homoTypicName == null) {
- return false;
- }
- HomotypicalGroup homotypicGroup = homoTypicName.getHomotypicalGroup();
- if (homotypicGroup == null || this.getHomotypicalGroup() == null) {
- return false;
- }
- if (homotypicGroup.equals(this.getHomotypicalGroup())) {
- return true;
- }
- return false;
- }
-
-
-
+ /**
+ * Returns the boolean value "false" since the components of <i>this</i> taxon name
+ * cannot follow the rules of a corresponding {@link NomenclaturalCode nomenclatural code}
+ * which is not defined for this class. The nomenclature code depends on
+ * the concrete name subclass ({@link BacterialName BacterialName},
+ * {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName},
+ * {@link ZoologicalName ZoologicalName} or {@link ViralName ViralName})
+ * to which a taxon name belongs.
+ *
+ * @return false
+ */
+ @Transient
+ public abstract boolean isCodeCompliant();
+
+ public abstract String generateFullTitle();
+
+
+
+ @Transient
+ public List<TaggedText> getTaggedName(){
+ return getCacheStrategy().getTaggedTitle(this);
+ }
+
+ @Transient
+ public String getFullTitleCache(){
+ if (protectedFullTitleCache){
+ return this.fullTitleCache;
+ }
+ if (fullTitleCache == null ){
+ this.fullTitleCache = getTruncatedCache(generateFullTitle());
+ }
+ return fullTitleCache;
+ }
+
+
+ public void setFullTitleCache(String fullTitleCache){
+ setFullTitleCache(fullTitleCache, PROTECTED);
+ }
+
+ public void setFullTitleCache(String fullTitleCache, boolean protectCache){
+ fullTitleCache = getTruncatedCache(fullTitleCache);
+ this.fullTitleCache = fullTitleCache;
+ this.setProtectedFullTitleCache(protectCache);
+ }
+
+
+ public boolean isProtectedFullTitleCache() {
+ return protectedFullTitleCache;
+ }
+
+ public void setProtectedFullTitleCache(boolean protectedFullTitleCache) {
+ this.protectedFullTitleCache = protectedFullTitleCache;
+ }
+
+ /**
+ * Returns the set of all {@link NameRelationship name relationships}
+ * in which <i>this</i> taxon name is involved. A taxon name can be both source
+ * in some name relationships or target in some others.
+ *
+ * @see #getRelationsToThisName()
+ * @see #getRelationsFromThisName()
+ * @see #addNameRelationship(NameRelationship)
+ * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
+ * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
+ */
+ @Transient
+ public Set<NameRelationship> getNameRelations() {
+ Set<NameRelationship> rels = new HashSet<NameRelationship>();
+ rels.addAll(getRelationsFromThisName());
+ rels.addAll(getRelationsToThisName());
+ return rels;
+ }
+
+ /**
+ * Creates a new {@link NameRelationship#NameRelationship(TaxonNameBase, TaxonNameBase, NameRelationshipType, String) name relationship} from <i>this</i> taxon name to another taxon name
+ * and adds it both to the set of {@link #getRelationsFromThisName() relations from <i>this</i> taxon name} and
+ * to the set of {@link #getRelationsToThisName() relations to the other taxon name}.
+ *
+ * @param toName the taxon name of the target for this new name relationship
+ * @param type the type of this new name relationship
+ * @param ruleConsidered the string which specifies the rule on which this name relationship is based
+ * @see #getRelationsToThisName()
+ * @see #getNameRelations()
+ * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
+ * @see #addNameRelationship(NameRelationship)
+ */
+ public void addRelationshipToName(TaxonNameBase toName, NameRelationshipType type, String ruleConsidered){
+ addRelationshipToName(toName, type, null, null, ruleConsidered);
+ // NameRelationship rel = new NameRelationship(toName, this, type, ruleConsidered);
+ }
+
+ /**
+ * Creates a new {@link NameRelationship#NameRelationship(TaxonNameBase, TaxonNameBase, NameRelationshipType, String) name relationship} from <i>this</i> taxon name to another taxon name
+ * and adds it both to the set of {@link #getRelationsFromThisName() relations from <i>this</i> taxon name} and
+ * to the set of {@link #getRelationsToThisName() relations to the other taxon name}.
+ *
+ * @param toName the taxon name of the target for this new name relationship
+ * @param type the type of this new name relationship
+ * @param ruleConsidered the string which specifies the rule on which this name relationship is based
+ * @return
+ * @see #getRelationsToThisName()
+ * @see #getNameRelations()
+ * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
+ * @see #addNameRelationship(NameRelationship)
+ */
+ public NameRelationship addRelationshipToName(TaxonNameBase toName, NameRelationshipType type, Reference citation, String microCitation, String ruleConsidered){
+ if (toName == null){
+ throw new NullPointerException("Null is not allowed as name for a name relationship");
+ }
+ NameRelationship rel = new NameRelationship(toName, this, type, citation, microCitation, ruleConsidered);
+ return rel;
+ }
+
+ /**
+ * Creates a new {@link NameRelationship#NameRelationship(TaxonNameBase, TaxonNameBase, NameRelationshipType, String) name relationship} from another taxon name to <i>this</i> taxon name
+ * and adds it both to the set of {@link #getRelationsToThisName() relations to <i>this</i> taxon name} and
+ * to the set of {@link #getRelationsFromThisName() relations from the other taxon name}.
+ *
+ * @param fromName the taxon name of the source for this new name relationship
+ * @param type the type of this new name relationship
+ * @param ruleConsidered the string which specifies the rule on which this name relationship is based
+ * @param citation the reference in which this relation was described
+ * @param microCitation the reference detail for this relation (e.g. page)
+ * @see #getRelationsFromThisName()
+ * @see #getNameRelations()
+ * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
+ * @see #addNameRelationship(NameRelationship)
+ */
+ public void addRelationshipFromName(TaxonNameBase fromName, NameRelationshipType type, String ruleConsidered){
+ fromName.addRelationshipToName(this, type, null, null, ruleConsidered);
+// NameRelationship rel = new NameRelationship(this, fromName, type, ruleConsidered);
+ }
+ /**
+ * Creates a new {@link NameRelationship#NameRelationship(TaxonNameBase, TaxonNameBase, NameRelationshipType, String) name relationship} from another taxon name to <i>this</i> taxon name
+ * and adds it both to the set of {@link #getRelationsToThisName() relations to <i>this</i> taxon name} and
+ * to the set of {@link #getRelationsFromThisName() relations from the other taxon name}.
+ *
+ * @param fromName the taxon name of the source for this new name relationship
+ * @param type the type of this new name relationship
+ * @param ruleConsidered the string which specifies the rule on which this name relationship is based
+ * @param citation the reference in which this relation was described
+ * @param microCitation the reference detail for this relation (e.g. page)
+ * @see #getRelationsFromThisName()
+ * @see #getNameRelations()
+ * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
+ * @see #addNameRelationship(NameRelationship)
+ */
+ public void addRelationshipFromName(TaxonNameBase fromName, NameRelationshipType type, Reference citation, String microCitation, String ruleConsidered){
+ fromName.addRelationshipToName(this, type, citation, microCitation, ruleConsidered);
+ }
+
+ /**
+ * Adds an existing {@link NameRelationship name relationship} either to the set of
+ * {@link #getRelationsToThisName() relations to <i>this</i> taxon name} or to the set of
+ * {@link #getRelationsFromThisName() relations from <i>this</i> taxon name}. If neither the
+ * source nor the target of the name relationship match with <i>this</i> taxon name
+ * no addition will be carried out.
+ *
+ * @param rel the name relationship to be added to one of <i>this</i> taxon name's name relationships sets
+ * @see #getNameRelations()
+ * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
+ * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
+ */
+ protected void addNameRelationship(NameRelationship rel) {
+ if (rel!=null && rel.getToName().equals(this)){
+ this.relationsToThisName.add(rel);
+ }else if(rel!=null && rel.getFromName().equals(this)){
+ this.relationsFromThisName.add(rel);
+ }else{
+ throw new RuntimeException("NameRelationship is either null or the relationship does not reference this name");
+ }
+ }
+ /**
+ * Removes one {@link NameRelationship name relationship} from one of both sets of
+ * {@link #getNameRelations() name relationships} in which <i>this</i> taxon name is involved.
+ * The name relationship will also be removed from one of both sets belonging
+ * to the second taxon name involved. Furthermore the fromName and toName
+ * attributes of the name relationship object will be nullified.
+ *
+ * @param nameRelation the name relationship which should be deleted from one of both sets
+ * @see #getNameRelations()
+ */
+ public void removeNameRelationship(NameRelationship nameRelation) {
+
+ TaxonNameBase fromName = nameRelation.getFromName();
+ TaxonNameBase toName = nameRelation.getToName();
+
+ if (nameRelation != null) {
+ nameRelation.setToName(null);
+ nameRelation.setFromName(null);
+ }
+
+ if (fromName != null) {
+ fromName.removeNameRelationship(nameRelation);
+ }
+
+ if (toName != null) {
+ toName.removeNameRelationship(nameRelation);
+ }
+
+ this.relationsToThisName.remove(nameRelation);
+ this.relationsFromThisName.remove(nameRelation);
+ }
+
+ public void removeRelationToTaxonName(TaxonNameBase toTaxonName) {
+ Set<NameRelationship> nameRelationships = new HashSet<NameRelationship>();
+// nameRelationships.addAll(this.getNameRelations());
+ nameRelationships.addAll(this.getRelationsFromThisName());
+ nameRelationships.addAll(this.getRelationsToThisName());
+ for(NameRelationship nameRelationship : nameRelationships) {
+ // remove name relationship from this side
+ if (nameRelationship.getFromName().equals(this) && nameRelationship.getToName().equals(toTaxonName)) {
+ this.removeNameRelationship(nameRelationship);
+ }
+ }
+ }
+
+
+ /**
+ * Does exactly the same as the addNameRelationship method provided that
+ * the given relationship is a name relationship.
+ *
+ * @param relation the relationship to be added to one of <i>this</i> taxon name's name relationships sets
+ * @see #addNameRelationship(NameRelationship)
+ * @see #getNameRelations()
+ * @see NameRelationship
+ * @see eu.etaxonomy.cdm.model.common.RelationshipBase
+ */
+ public void addRelationship(RelationshipBase relation) {
+ if (relation instanceof NameRelationship){
+ addNameRelationship((NameRelationship)relation);
+ NameRelationshipType type = (NameRelationshipType)relation.getType();
+ if (type != null && ( type.isBasionymRelation() || type.isReplacedSynonymRelation() ) ){
+ TaxonNameBase fromName = ((NameRelationship)relation).getFromName();
+ TaxonNameBase toName = ((NameRelationship)relation).getToName();
+ fromName.mergeHomotypicGroups(toName);
+ }
+ }else{
+ logger.warn("Relationship not of type NameRelationship!");
+ throw new IllegalArgumentException("Relationship not of type NameRelationship");
+ }
+ }
+
+
+ /**
+ * Returns the set of all {@link NameRelationship name relationships}
+ * in which <i>this</i> taxon name is involved as a source ("from"-side).
+ *
+ * @see #getNameRelations()
+ * @see #getRelationsToThisName()
+ * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
+ */
+ public Set<NameRelationship> getRelationsFromThisName() {
+ if(relationsFromThisName == null) {
+ this.relationsFromThisName = new HashSet<NameRelationship>();
+ }
+ return relationsFromThisName;
+ }
+
+ /**
+ * Returns the set of all {@link NameRelationship name relationships}
+ * in which <i>this</i> taxon name is involved as a target ("to"-side).
+ *
+ * @see #getNameRelations()
+ * @see #getRelationsFromThisName()
+ * @see #addRelationshipToName(TaxonNameBase, NameRelationshipType, String)
+ */
+ public Set<NameRelationship> getRelationsToThisName() {
+ if(relationsToThisName == null) {
+ this.relationsToThisName = new HashSet<NameRelationship>();
+ }
+ return relationsToThisName;
+ }
+
+ /**
+ * Returns the set of {@link NomenclaturalStatus nomenclatural status} assigned
+ * to <i>this</i> taxon name according to its corresponding nomenclature code.
+ * This includes the {@link NomenclaturalStatusType type} of the nomenclatural status
+ * and the nomenclatural code rule considered.
+ *
+ * @see NomenclaturalStatus
+ * @see NomenclaturalStatusType
+ */
+ public Set<NomenclaturalStatus> getStatus() {
+ if(status == null) {
+ this.status = new HashSet<NomenclaturalStatus>();
+ }
+ return status;
+ }
+
+ /**
+ * Adds a new {@link NomenclaturalStatus nomenclatural status}
+ * to <i>this</i> taxon name's set of nomenclatural status.
+ *
+ * @param nomStatus the nomenclatural status to be added
+ * @see #getStatus()
+ */
+ public void addStatus(NomenclaturalStatus nomStatus) {
+ this.status.add(nomStatus);
+ }
+
+ /**
+ * Removes one element from the set of nomenclatural status of <i>this</i> taxon name.
+ * Type and ruleConsidered attributes of the nomenclatural status object
+ * will be nullified.
+ *
+ * @param nomStatus the nomenclatural status of <i>this</i> taxon name which should be deleted
+ * @see #getStatus()
+ */
+ public void removeStatus(NomenclaturalStatus nomStatus) {
+ //TODO to be implemented?
+ logger.warn("not yet fully implemented?");
+ this.status.remove(nomStatus);
+ }
+
+
+ /**
+ * Indicates whether <i>this</i> taxon name is a {@link NameRelationshipType#BASIONYM() basionym}
+ * or a {@link NameRelationshipType#REPLACED_SYNONYM() replaced synonym}
+ * of any other taxon name. Returns "true", if a basionym or a replaced
+ * synonym {@link NameRelationship relationship} from <i>this</i> taxon name to another taxon name exists,
+ * false otherwise (also in case <i>this</i> taxon name is the only one in the
+ * homotypical group).
+ */
+ @Transient
+ public boolean isOriginalCombination(){
+ Set<NameRelationship> relationsFromThisName = this.getRelationsFromThisName();
+ for (NameRelationship relation : relationsFromThisName) {
+ if (relation.getType().isBasionymRelation() ||
+ relation.getType().isReplacedSynonymRelation()) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Returns the taxon name which is the {@link NameRelationshipType#BASIONYM() basionym} of <i>this</i> taxon name.
+ * The basionym of a taxon name is its epithet-bringing synonym.
+ * For instance <i>Pinus abies</i> L. was published by Linnaeus and the botanist
+ * Karsten transferred later <i>this</i> taxon to the genus Picea. Therefore,
+ * <i>Pinus abies</i> L. is the basionym of the new combination <i>Picea abies</i> (L.) H. Karst.
+ *
+ * If more than one basionym exists one is choosen at radom.
+ *
+ * If no basionym exists null is returned.
+ */
+ @Transient
+ public TaxonNameBase getBasionym(){
+ Set<TaxonNameBase> basionyms = getBasionyms();
+ if (basionyms.size() == 0){
+ return null;
+ }else{
+ return basionyms.iterator().next();
+ }
+ }
+
+ /**
+ * Returns the set of taxon names which are the {@link NameRelationshipType#BASIONYM() basionyms} of <i>this</i> taxon name.
+ * The basionym of a taxon name is its epithet-bringing synonym.
+ * For instance <i>Pinus abies</i> L. was published by Linnaeus and the botanist
+ * Karsten transferred later <i>this</i> taxon to the genus Picea. Therefore,
+ * <i>Pinus abies</i> L. is the basionym of the new combination <i>Picea abies</i> (L.) H. Karst.
+ */
+ @Transient
+ public Set<TaxonNameBase> getBasionyms(){
+ Set<TaxonNameBase> result = new HashSet<TaxonNameBase>();
+ Set<NameRelationship> rels = this.getRelationsToThisName();
+ for (NameRelationship rel : rels){
+ if (rel.getType().isBasionymRelation()){
+ TaxonNameBase basionym = rel.getFromName();
+ result.add(basionym);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Assigns a taxon name as {@link NameRelationshipType#BASIONYM() basionym} of <i>this</i> taxon name.
+ * The basionym {@link NameRelationship relationship} will be added to <i>this</i> taxon name
+ * and to the basionym. The basionym cannot have itself a basionym.
+ * The {@link HomotypicalGroup homotypical groups} of <i>this</i> taxon name and of the basionym
+ * will be {@link HomotypicalGroup#merge(HomotypicalGroup) merged}.
+ *
+ * @param basionym the taxon name to be set as the basionym of <i>this</i> taxon name
+ * @see #getBasionym()
+ * @see #addBasionym(TaxonNameBase, String)
+ */
+ public void addBasionym(T basionym){
+ addBasionym(basionym, null, null, null);
+ }
+ /**
+ * Assigns a taxon name as {@link NameRelationshipType#BASIONYM() basionym} of <i>this</i> taxon name
+ * and keeps the nomenclatural rule considered for it. The basionym
+ * {@link NameRelationship relationship} will be added to <i>this</i> taxon name and to the basionym.
+ * The basionym cannot have itself a basionym.
+ * The {@link HomotypicalGroup homotypical groups} of <i>this</i> taxon name and of the basionym
+ * will be {@link HomotypicalGroup#merge(HomotypicalGroup) merged}.
+ *
+ * @param basionym the taxon name to be set as the basionym of <i>this</i> taxon name
+ * @param ruleConsidered the string identifying the nomenclatural rule
+ * @return
+ * @see #getBasionym()
+ * @see #addBasionym(TaxonNameBase)
+ */
+ public NameRelationship addBasionym(T basionym, Reference citation, String microcitation, String ruleConsidered){
+ if (basionym != null){
+ return basionym.addRelationshipToName(this, NameRelationshipType.BASIONYM(), citation, microcitation, ruleConsidered);
+ }else{
+ return null;
+ }
+ }
+
+ /**
+ * Assigns a taxon name as {@link NameRelationshipType#REPLACED_SYNONYM() replaced synonym} of <i>this</i> taxon name
+ * and keeps the nomenclatural rule considered for it. The replaced synonym
+ * {@link NameRelationship relationship} will be added to <i>this</i> taxon name and to the replaced synonym.
+ * The {@link HomotypicalGroup homotypical groups} of <i>this</i> taxon name and of the replaced synonym
+ * will be {@link HomotypicalGroup#merge(HomotypicalGroup) merged}.
+ *
+ * @param basionym the taxon name to be set as the basionym of <i>this</i> taxon name
+ * @param ruleConsidered the string identifying the nomenclatural rule
+ * @see #getBasionym()
+ * @see #addBasionym(TaxonNameBase)
+ */
+ //TODO: Check if true: The replaced synonym cannot have itself a replaced synonym (?).
+ public void addReplacedSynonym(T replacedSynonym, Reference citation, String microcitation, String ruleConsidered){
+ if (replacedSynonym != null){
+ replacedSynonym.addRelationshipToName(this, NameRelationshipType.REPLACED_SYNONYM(), citation, microcitation, ruleConsidered);
+ }
+ }
+
+ /**
+ * Removes the {@link NameRelationshipType#BASIONYM() basionym} {@link NameRelationship relationship} from the set of
+ * {@link #getRelationsToThisName() name relationships to} <i>this</i> taxon name. The same relationhip will be
+ * removed from the set of {@link #getRelationsFromThisName() name relationships from} the taxon name
+ * previously used as basionym.
+ *
+ * @see #getBasionym()
+ * @see #addBasionym(TaxonNameBase)
+ */
+ public void removeBasionyms(){
+ Set<NameRelationship> removeRelations = new HashSet<NameRelationship>();
+ for (NameRelationship nameRelation : this.getRelationsToThisName()){
+ if (nameRelation.getType().isBasionymRelation()){
+ removeRelations.add(nameRelation);
+ }
+ }
+ // Removing relations from a set through which we are iterating causes a
+ // ConcurrentModificationException. Therefore, we delete the targeted
+ // relations in a second step.
+ for (NameRelationship relation : removeRelations){
+ this.removeNameRelationship(relation);
+ }
+ }
+
+ /**
+ * Returns the taxonomic {@link Rank rank} of <i>this</i> taxon name.
+ *
+ * @see Rank
+ */
+ public Rank getRank(){
+ return this.rank;
+ }
+
+ /**
+ * @see #getRank()
+ */
+ public void setRank(Rank rank){
+ this.rank = rank;
+ }
+
+ /**
+ * Returns the {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} of <i>this</i> taxon name.
+ * The nomenclatural reference is here meant to be the one publication
+ * <i>this</i> taxon name was originally published in while fulfilling the formal
+ * requirements as specified by the corresponding {@link NomenclaturalCode nomenclatural code}.
+ *
+ * @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference
+ * @see eu.etaxonomy.cdm.model.reference.Reference
+ */
+ public INomenclaturalReference getNomenclaturalReference(){
+ return this.nomenclaturalReference;
+ }
+ /**
+ * Assigns a {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} to <i>this</i> taxon name.
+ * The corresponding {@link eu.etaxonomy.cdm.model.reference.Reference.isNomenclaturallyRelevant nomenclaturally relevant flag} will be set to true
+ * as it is obviously used for nomenclatural purposes.
+ *
+ * @throws IllegalArgumentException if parameter <code>nomenclaturalReference</code> is not assignable from {@link INomenclaturalReference}
+ * @see #getNomenclaturalReference()
+ */
+ public void setNomenclaturalReference(INomenclaturalReference nomenclaturalReference){
+ if(nomenclaturalReference != null){
+ if(!INomenclaturalReference.class.isAssignableFrom(nomenclaturalReference.getClass())){
+ throw new IllegalArgumentException("Parameter nomenclaturalReference is not assignable from INomenclaturalReference");
+ }
+ this.nomenclaturalReference = (Reference)nomenclaturalReference;
+ } else {
+ this.nomenclaturalReference = null;
+ }
+ }
+
+ /**
+ * Returns the appended phrase string assigned to <i>this</i> taxon name.
+ * The appended phrase is a non-atomised addition to a name. It is
+ * not ruled by a nomenclatural code.
+ */
+ public String getAppendedPhrase(){
+ return this.appendedPhrase;
+ }
+
+ /**
+ * @see #getAppendedPhrase()
+ */
+ public void setAppendedPhrase(String appendedPhrase){
+ this.appendedPhrase = appendedPhrase;
+ }
+
+ /**
+ * Returns the details string of the {@link #getNomenclaturalReference() nomenclatural reference} assigned
+ * to <i>this</i> taxon name. The details describe the exact localisation within
+ * the publication used as nomenclature reference. These are mostly
+ * (implicitly) pages but can also be figures or tables or any other
+ * element of a publication. A nomenclatural micro reference (details)
+ * requires the existence of a nomenclatural reference.
+ */
+ //Details of the nomenclatural reference (protologue).
+ public String getNomenclaturalMicroReference(){
+ return this.nomenclaturalMicroReference;
+ }
+ /**
+ * @see #getNomenclaturalMicroReference()
+ */
+ public void setNomenclaturalMicroReference(String nomenclaturalMicroReference){
+ this.nomenclaturalMicroReference = nomenclaturalMicroReference;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IParsable#getHasProblem()
+ */
+ public int getParsingProblem(){
+ return this.parsingProblem;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IParsable#setHasProblem(int)
+ */
+ public void setParsingProblem(int parsingProblem){
+ this.parsingProblem = parsingProblem;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IParsable#addProblem(eu.etaxonomy.cdm.strategy.parser.NameParserWarning)
+ */
+ public void addParsingProblem(ParserProblem problem){
+ parsingProblem = ParserProblem.addProblem(parsingProblem, problem);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IParsable#removeParsingProblem(eu.etaxonomy.cdm.strategy.parser.ParserProblem)
+ */
+ public void removeParsingProblem(ParserProblem problem) {
+ parsingProblem = ParserProblem.removeProblem(parsingProblem, problem);
+ }
+
+ /**
+ * @param warnings
+ */
+ public void addParsingProblems(int problems){
+ parsingProblem = ParserProblem.addProblems(parsingProblem, problems);
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IParsable#hasProblem()
+ */
+ public boolean hasProblem(){
+ return parsingProblem != 0;
+ }
+
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IParsable#hasProblem(eu.etaxonomy.cdm.strategy.parser.ParserProblem)
+ */
+ public boolean hasProblem(ParserProblem problem) {
+ return getParsingProblems().contains(problem);
+ }
+
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IParsable#problemStarts()
+ */
+ public int getProblemStarts(){
+ return this.problemStarts;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IParsable#setProblemStarts(int)
+ */
+ public void setProblemStarts(int start) {
+ this.problemStarts = start;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IParsable#problemEnds()
+ */
+ public int getProblemEnds(){
+ return this.problemEnds;
+ }
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IParsable#setProblemEnds(int)
+ */
+ public void setProblemEnds(int end) {
+ this.problemEnds = end;
+ }
+
+//*********************** TYPE DESIGNATION *********************************************//
+
+ /**
+ * Returns the set of {@link TypeDesignationBase type designations} assigned
+ * to <i>this</i> taxon name.
+ * @see NameTypeDesignation
+ * @see SpecimenTypeDesignation
+ */
+ public Set<TypeDesignationBase> getTypeDesignations() {
+ if(typeDesignations == null) {
+ this.typeDesignations = new HashSet<TypeDesignationBase>();
+ }
+ return typeDesignations;
+ }
+
+ /**
+ * Removes one element from the set of {@link TypeDesignationBase type designations} assigned to
+ * <i>this</i> taxon name. The type designation itself will be nullified.
+ *
+ * @param typeDesignation the type designation which should be deleted
+ */
+ @SuppressWarnings("deprecation")
+ public void removeTypeDesignation(TypeDesignationBase typeDesignation) {
+ this.typeDesignations.remove(typeDesignation);
+ typeDesignation.removeTypifiedName(this);
+ }
+
+ /**
+ * Returns the set of {@link SpecimenTypeDesignation specimen type designations} assigned
+ * to <i>this</i> taxon name. The {@link Rank rank} of <i>this</i> taxon name is generally
+ * "species" or below. The specimen type designations include all the
+ * specimens on which the typification of this name is based (which are
+ * exclusively used to typify taxon names belonging to the same
+ * {@link HomotypicalGroup homotypical group} to which <i>this</i> taxon name
+ * belongs) and eventually the status of these designations.
+ *
+ * @see SpecimenTypeDesignation
+ * @see NameTypeDesignation
+ * @see HomotypicalGroup
+ */
+ @Transient
+ public Set<SpecimenTypeDesignation> getSpecimenTypeDesignationsOfHomotypicalGroup() {
+ return this.getHomotypicalGroup().getSpecimenTypeDesignations();
+ }
+
+//*********************** NAME TYPE DESIGNATION *********************************************//
+
+ /**
+ * Returns the set of {@link NameTypeDesignation name type designations} assigned
+ * to <i>this</i> taxon name the rank of which must be above "species".
+ * The name type designations include all the taxon names used to typify
+ * <i>this</i> taxon name and eventually the rejected or conserved status
+ * of these designations.
+ *
+ * @see NameTypeDesignation
+ * @see SpecimenTypeDesignation
+ */
+ @Transient
+ public Set<NameTypeDesignation> getNameTypeDesignations() {
+ Set<NameTypeDesignation> result = new HashSet<NameTypeDesignation>();
+ for (TypeDesignationBase typeDesignation : this.typeDesignations){
+ if (typeDesignation instanceof NameTypeDesignation){
+ result.add((NameTypeDesignation)typeDesignation);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Creates and adds a new {@link NameTypeDesignation name type designation}
+ * to <i>this</i> taxon name's set of type designations.
+ *
+ * @param typeSpecies the taxon name to be used as type of <i>this</i> taxon name
+ * @param citation the reference for this new designation
+ * @param citationMicroReference the string with the details (generally pages) within the reference
+ * @param originalNameString the taxon name string used in the reference to assert this designation
+ * @param isRejectedType the boolean status for a rejected name type designation
+ * @param isConservedType the boolean status for a conserved name type designation
+ * @param isLectoType the boolean status for a lectotype name type designation
+ * @param isNotDesignated the boolean status for a name type designation without name type
+ * @param addToAllHomotypicNames the boolean indicating whether the name type designation should be
+ * added to all taxon names of the homotypical group this taxon name belongs to
+ * @return
+ * @see #getNameTypeDesignations()
+ * @see NameTypeDesignation
+ * @see TypeDesignationBase#isNotDesignated()
+ */
+ public NameTypeDesignation addNameTypeDesignation(TaxonNameBase typeSpecies,
+ Reference citation,
+ String citationMicroReference,
+ String originalNameString,
+ NameTypeDesignationStatus status,
+ boolean isRejectedType,
+ boolean isConservedType,
+ /*boolean isLectoType, */
+ boolean isNotDesignated,
+ boolean addToAllHomotypicNames) {
+ NameTypeDesignation nameTypeDesignation = new NameTypeDesignation(typeSpecies, citation, citationMicroReference, originalNameString, status, isRejectedType, isConservedType, isNotDesignated);
+ //nameTypeDesignation.setLectoType(isLectoType);
+ addTypeDesignation(nameTypeDesignation, addToAllHomotypicNames);
+ return nameTypeDesignation;
+ }
+
+ /**
+ * Creates and adds a new {@link NameTypeDesignation name type designation}
+ * to <i>this</i> taxon name's set of type designations.
+ *
+ * @param typeSpecies the taxon name to be used as type of <i>this</i> taxon name
+ * @param citation the reference for this new designation
+ * @param citationMicroReference the string with the details (generally pages) within the reference
+ * @param originalNameString the taxon name string used in the reference to assert this designation
+ * @param status the name type designation status
+ * @param addToAllHomotypicNames the boolean indicating whether the name type designation should be
+ * added to all taxon names of the homotypical group this taxon name belongs to
+ * @return
+ * @see #getNameTypeDesignations()
+ * @see NameTypeDesignation
+ * @see TypeDesignationBase#isNotDesignated()
+ */
+ public NameTypeDesignation addNameTypeDesignation(TaxonNameBase typeSpecies,
+ Reference citation,
+ String citationMicroReference,
+ String originalNameString,
+ NameTypeDesignationStatus status,
+ boolean addToAllHomotypicNames) {
+ NameTypeDesignation nameTypeDesignation = new NameTypeDesignation(typeSpecies, status, citation, citationMicroReference, originalNameString);
+ addTypeDesignation(nameTypeDesignation, addToAllHomotypicNames);
+ return nameTypeDesignation;
+ }
+
+//*********************** SPECIMEN TYPE DESIGNATION *********************************************//
+
+ /**
+ * Returns the set of {@link SpecimenTypeDesignation specimen type designations}
+ * that typify <i>this</i> taxon name.
+ */
+ @Transient
+ public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations() {
+ Set<SpecimenTypeDesignation> result = new HashSet<SpecimenTypeDesignation>();
+ for (TypeDesignationBase typeDesignation : this.typeDesignations){
+ if (typeDesignation instanceof SpecimenTypeDesignation){
+ result.add((SpecimenTypeDesignation)typeDesignation);
+ }
+ }
+ return result;
+ }
+
+
+ /**
+ * Creates and adds a new {@link SpecimenTypeDesignation specimen type designation}
+ * to <i>this</i> taxon name's set of type designations.
+ *
+ * @param typeSpecimen the specimen to be used as a type for <i>this</i> taxon name
+ * @param status the specimen type designation status
+ * @param citation the reference for this new specimen type designation
+ * @param citationMicroReference the string with the details (generally pages) within the reference
+ * @param originalNameString the taxon name used in the reference to assert this designation
+ * @param isNotDesignated the boolean status for a specimen type designation without specimen type
+ * @param addToAllHomotypicNames the boolean indicating whether the specimen type designation should be
+ * added to all taxon names of the homotypical group the typified
+ * taxon name belongs to
+ * @return
+ * @see #getSpecimenTypeDesignations()
+ * @see SpecimenTypeDesignationStatus
+ * @see SpecimenTypeDesignation
+ * @see TypeDesignationBase#isNotDesignated()
+ */
+ public SpecimenTypeDesignation addSpecimenTypeDesignation(Specimen typeSpecimen,
+ SpecimenTypeDesignationStatus status,
+ Reference citation,
+ String citationMicroReference,
+ String originalNameString,
+ boolean isNotDesignated,
+ boolean addToAllHomotypicNames) {
+ SpecimenTypeDesignation specimenTypeDesignation = new SpecimenTypeDesignation(typeSpecimen, status, citation, citationMicroReference, originalNameString, isNotDesignated);
+ addTypeDesignation(specimenTypeDesignation, addToAllHomotypicNames);
+ return specimenTypeDesignation;
+ }
+
+ //used by merge strategy
+ private boolean addTypeDesignation(TypeDesignationBase typeDesignation){
+ return addTypeDesignation(typeDesignation, true);
+ }
+
+ /**
+ * Adds a {@link TypeDesignationBase type designation} to <code>this</code> taxon name's set of type designations
+ *
+ * @param typeDesignation the typeDesignation to be added to <code>this</code> taxon name
+ * @param addToAllNames the boolean indicating whether the type designation should be
+ * added to all taxon names of the homotypical group the typified
+ * taxon name belongs to
+ * @return true if the operation was succesful
+ *
+ * @throws IllegalArgumentException if the type designation already has typified names, an {@link IllegalArgumentException exception}
+ * is thrown. We do this to prevent a type designation to be used for multiple taxon names.
+ *
+ */
+ public boolean addTypeDesignation(TypeDesignationBase typeDesignation, boolean addToAllNames){
+ //currently typeDesignations are not persisted with the homotypical group
+ //so explicit adding to the homotypical group is not necessary.
+ if (typeDesignation != null){
+ checkHomotypicalGroup(typeDesignation);
+ this.typeDesignations.add(typeDesignation);
+ typeDesignation.addTypifiedName(this);
+
+ if (addToAllNames){
+ for (TaxonNameBase taxonName : this.getHomotypicalGroup().getTypifiedNames()){
+ if (taxonName != this){
+ taxonName.addTypeDesignation(typeDesignation, false);
+ }
+ }
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Throws an Exception this type designation already has typified names from another homotypical group.
+ * @param typeDesignation
+ */
+ private void checkHomotypicalGroup(TypeDesignationBase typeDesignation) {
+ if(typeDesignation.getTypifiedNames().size() > 0){
+ Set<HomotypicalGroup> groups = new HashSet<HomotypicalGroup>();
+ Set<TaxonNameBase> names = typeDesignation.getTypifiedNames();
+ for (TaxonNameBase taxonName: names){
+ groups.add(taxonName.getHomotypicalGroup());
+ }
+ if (groups.size() > 1){
+ throw new IllegalArgumentException("TypeDesignation already has typified names from another homotypical group.");
+ }
+ }
+ }
+
+
+
+//*********************** HOMOTYPICAL GROUP *********************************************//
+
+
+ /**
+ * Returns the {@link HomotypicalGroup homotypical group} to which
+ * <i>this</i> taxon name belongs. A homotypical group represents all taxon names
+ * that share the same types.
+ *
+ * @see HomotypicalGroup
+ */
+
+ public HomotypicalGroup getHomotypicalGroup() {
+ return homotypicalGroup;
+ }
+
+ /*
+ * @see #getHomotypicalGroup()
+ */
+ public void setHomotypicalGroup(HomotypicalGroup homotypicalGroup) {
+ if (homotypicalGroup == null){
+ throw new IllegalArgumentException("HomotypicalGroup of name should never be null but was set to 'null'");
+ }
+ this.homotypicalGroup = homotypicalGroup;
+ if (! homotypicalGroup.typifiedNames.contains(this)){
+ homotypicalGroup.addTypifiedName(this);
+ }
+ }
+
+
+
+// *************************************************************************//
+
+ /**
+ * @see #getNomenclaturalReference()
+ */
+ @Transient
+ public Reference getCitation(){
+ //TODO What is the purpose of this method differing from the getNomenclaturalReference method?
+ logger.warn("getCitation not yet implemented");
+ return null;
+ }
+
+ /**
+ * Returns the complete string containing the
+ * {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference#getNomenclaturalCitation() nomenclatural reference citation}
+ * and the {@link #getNomenclaturalMicroReference() details} assigned to <i>this</i> taxon name.
+ *
+ * @return the string containing the nomenclatural reference of <i>this</i> taxon name
+ * @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference#getNomenclaturalCitation()
+ * @see #getNomenclaturalReference()
+ * @see #getNomenclaturalMicroReference()
+ */
+ @Transient
+ public String getCitationString(){
+ return getNomenclaturalReference().getNomenclaturalCitation(getNomenclaturalMicroReference());
+ }
+
+ /**
+ * Returns the parsing problems
+ * @return
+ */
+ public List<ParserProblem> getParsingProblems(){
+ return ParserProblem.warningList(this.parsingProblem);
+ }
+
+ /**
+ * Returns the string containing the publication date (generally only year)
+ * of the {@link #getNomenclaturalReference() nomenclatural reference} for <i>this</i> taxon name, null if there is
+ * no nomenclatural reference.
+ *
+ * @return the string containing the publication date of <i>this</i> taxon name
+ * @see eu.etaxonomy.cdm.model.reference.INomenclaturalReference#getYear()
+ */
+ @Transient
+ public String getReferenceYear(){
+ if (this.getNomenclaturalReference() != null ){
+ return this.getNomenclaturalReference().getYear();
+ }else{
+ return null;
+ }
+ }
+
+ /**
+ * Returns the set of {@link eu.etaxonomy.cdm.model.taxon.TaxonBase taxon bases} that refer to <i>this</i> taxon name.
+ * In this context a taxon base means the use of a taxon name by a reference
+ * either as a {@link eu.etaxonomy.cdm.model.taxon.Taxon taxon} ("accepted/correct" name) or
+ * as a (junior) {@link eu.etaxonomy.cdm.model.taxon.Synonym synonym}.
+ * A taxon name can be used by several distinct {@link eu.etaxonomy.cdm.model.reference.Reference references} but only once
+ * within a taxonomic treatment (identified by one reference).
+ *
+ * @see #getTaxa()
+ * @see #getSynonyms()
+ */
+ public Set<TaxonBase> getTaxonBases() {
+ if(taxonBases == null) {
+ this.taxonBases = new HashSet<TaxonBase>();
+ }
+ return this.taxonBases;
+ }
+
+ /**
+ * Adds a new {@link eu.etaxonomy.cdm.model.taxon.TaxonBase taxon base}
+ * to the set of taxon bases using <i>this</i> taxon name.
+ *
+ * @param taxonBase the taxon base to be added
+ * @see #getTaxonBases()
+ * @see #removeTaxonBase(TaxonBase)
+ */
+ //TODO protected
+ public void addTaxonBase(TaxonBase taxonBase){
+ Method method = ReflectionUtils.findMethod(TaxonBase.class, "setName", new Class[] {TaxonNameBase.class});
+ ReflectionUtils.makeAccessible(method);
+ ReflectionUtils.invokeMethod(method, taxonBase, new Object[] {this});
+ taxonBases.add(taxonBase);
+ }
+ /**
+ * Removes one element from the set of {@link eu.etaxonomy.cdm.model.taxon.TaxonBase taxon bases} that refer to <i>this</i> taxon name.
+ *
+ * @param taxonBase the taxon base which should be removed from the corresponding set
+ * @see #getTaxonBases()
+ * @see #addTaxonBase(TaxonBase)
+ */
+ public void removeTaxonBase(TaxonBase taxonBase){
+ Method method = ReflectionUtils.findMethod(TaxonBase.class, "setName", new Class[] {TaxonNameBase.class});
+ ReflectionUtils.makeAccessible(method);
+ ReflectionUtils.invokeMethod(method, taxonBase, new Object[] {null});
+ taxonBases.remove(taxonBase);
+ }
+
+ /**
+ * Returns the set of {@link eu.etaxonomy.cdm.model.taxon.Taxon taxa} ("accepted/correct" names according to any
+ * reference) that are based on <i>this</i> taxon name. This set is a subset of
+ * the set returned by getTaxonBases().
+ *
+ * @see eu.etaxonomy.cdm.model.taxon.Taxon
+ * @see #getTaxonBases()
+ * @see #getSynonyms()
+ */
+ @Transient
+ public Set<Taxon> getTaxa(){
+ Set<Taxon> result = new HashSet<Taxon>();
+ for (TaxonBase taxonBase : this.taxonBases){
+ if (taxonBase instanceof Taxon){
+ result.add((Taxon)taxonBase);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns the set of {@link eu.etaxonomy.cdm.model.taxon.Synonym (junior) synonyms} (according to any
+ * reference) that are based on <i>this</i> taxon name. This set is a subset of
+ * the set returned by getTaxonBases().
+ *
+ * @see eu.etaxonomy.cdm.model.taxon.Synonym
+ * @see #getTaxonBases()
+ * @see #getTaxa()
+ */
+ @Transient
+ public Set<Synonym> getSynonyms() {
+ Set<Synonym> result = new HashSet<Synonym>();
+ for (TaxonBase taxonBase : this.taxonBases){
+ if (taxonBase instanceof Synonym){
+ result.add((Synonym)taxonBase);
+ }
+ }
+ return result;
+ }
+
+
+// *********** DESCRIPTIONS *************************************
+
+ /**
+ * Returns the set of {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription taxon name descriptions} assigned
+ * to <i>this</i> taxon name. A taxon name description is a piece of information
+ * concerning the taxon name like for instance the content of its first
+ * publication (protolog) or a picture of this publication.
+ *
+ * @see #addDescription(TaxonNameDescription)
+ * @see #removeDescription(TaxonNameDescription)
+ * @see eu.etaxonomy.cdm.model.description.TaxonNameDescription
+ */
+ public Set<TaxonNameDescription> getDescriptions() {
+ return descriptions;
+ }
+
+ /**
+ * Adds a new {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription taxon name description}
+ * to the set of taxon name descriptions assigned to <i>this</i> taxon name. The
+ * content of the {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription#getTaxonName() taxonName attribute} of the
+ * taxon name description itself will be replaced with <i>this</i> taxon name.
+ *
+ * @param description the taxon name description to be added
+ * @see #getDescriptions()
+ * @see #removeDescription(TaxonNameDescription)
+ */
+ public void addDescription(TaxonNameDescription description) {
+ java.lang.reflect.Field field = ReflectionUtils.findField(TaxonNameDescription.class, "taxonName", TaxonNameBase.class);
+ ReflectionUtils.makeAccessible(field);
+ ReflectionUtils.setField(field, description, this);
+ descriptions.add(description);
+ }
+ /**
+ * Removes one element from the set of {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription taxon name descriptions} assigned
+ * to <i>this</i> taxon name. The content of the {@link eu.etaxonomy.cdm.model.description.TaxonNameDescription#getTaxonName() taxonName attribute}
+ * of the description itself will be set to "null".
+ *
+ * @param description the taxon name description which should be removed
+ * @see #getDescriptions()
+ * @see #addDescription(TaxonNameDescription)
+ * @see eu.etaxonomy.cdm.model.description.TaxonNameDescription#getTaxonName()
+ */
+ public void removeDescription(TaxonNameDescription description) {
+ java.lang.reflect.Field field = ReflectionUtils.findField(TaxonNameDescription.class, "taxonName", TaxonNameBase.class);
+ ReflectionUtils.makeAccessible(field);
+ ReflectionUtils.setField(field, description, null);
+ descriptions.remove(description);
+ }
+
+// *********** HOMOTYPIC GROUP METHODS **************************************************
+
+ @Transient
+ public void mergeHomotypicGroups(TaxonNameBase name){
+ this.getHomotypicalGroup().merge(name.getHomotypicalGroup());
+ //HomotypicalGroup thatGroup = name.homotypicalGroup;
+ name.setHomotypicalGroup(this.homotypicalGroup);
+ }
+
+ /**
+ * Returns the boolean value indicating whether a given taxon name belongs
+ * to the same {@link HomotypicalGroup homotypical group} as <i>this</i> taxon name (true)
+ * or not (false). Returns "true" only if the homotypical groups of both
+ * taxon names exist and if they are identical.
+ *
+ * @param homoTypicName the taxon name the homotypical group of which is to be checked
+ * @return the boolean value of the check
+ * @see HomotypicalGroup
+ */
+ @Transient
+ public boolean isHomotypic(TaxonNameBase homoTypicName) {
+ if (homoTypicName == null) {
+ return false;
+ }
+ HomotypicalGroup homotypicGroup = homoTypicName.getHomotypicalGroup();
+ if (homotypicGroup == null || this.getHomotypicalGroup() == null) {
+ return false;
+ }
+ if (homotypicGroup.equals(this.getHomotypicalGroup())) {
+ return true;
+ }
+ return false;
+ }
+
+
+ /**
+ * Checks whether name is a basionym for ALL names
+ * in its homotypical group.
+ * Returns <code>false</code> if there are no other names in the group
+ * @param name
+ * @return
+ */
+ @Transient
+ public boolean isGroupsBasionym() {
+ Set<TaxonNameBase> typifiedNames = homotypicalGroup.getTypifiedNames();
+
+ // Check whether there are any other names in the group
+ if (typifiedNames.size() == 1) {
+ return false;
+ }
+
+ boolean isBasionymToAll = true;
+
+ for (TaxonNameBase taxonName : typifiedNames) {
+ if (!taxonName.equals(this)) {
+ if (! isBasionymFor(taxonName)) {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Checks whether a basionym relationship exists between fromName and toName.
+ *
+ * @param fromName
+ * @param toName
+ * @return
+ */
+ @Transient
+ public boolean isBasionymFor(TaxonNameBase newCombinationName) {
+ Set<NameRelationship> relations = newCombinationName.getRelationsToThisName();
+ for (NameRelationship relation : relations) {
+ if (relation.getType().equals(NameRelationshipType.BASIONYM()) &&
+ relation.getFromName().equals(this)) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Creates a basionym relationship to all other names in this names homotypical
+ * group.
+ *
+ * @see HomotypicalGroup.setGroupBasionym(TaxonNameBase basionymName)
+
+ */
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.name.HomotypicalGroup#setGroupBasionym(TaxonNameBase)
+ */
+ @Transient
+ public void makeGroupsBasionym() {
+ this.homotypicalGroup.setGroupBasionym(this);
+ }
+
+
//********* Rank comparison shortcuts ********************//
- /**
- * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
- * taxon name is higher than the genus rank (true) or not (false).
- * Suprageneric non viral names are monomials.
- * Returns false if rank is null.
- *
- * @see #isGenus()
- * @see #isInfraGeneric()
- * @see #isSpecies()
- * @see #isInfraSpecific()
- */
- @Transient
- public boolean isSupraGeneric() {
- if (rank == null){
- return false;
- }
- return getRank().isSupraGeneric();
- }
- /**
- * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
- * taxon name is the genus rank (true) or not (false). Non viral names with
- * genus rank are monomials. Returns false if rank is null.
- *
- * @see #isSupraGeneric()
- * @see #isInfraGeneric()
- * @see #isSpecies()
- * @see #isInfraSpecific()
- */
- @Transient
- public boolean isGenus() {
- if (rank == null){
- return false;
- }
- return getRank().isGenus();
- }
- /**
- * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
- * taxon name is higher than the species rank and lower than the
- * genus rank (true) or not (false). Infrageneric non viral names are
- * binomials. Returns false if rank is null.
- *
- * @see #isSupraGeneric()
- * @see #isGenus()
- * @see #isSpecies()
- * @see #isInfraSpecific()
- */
- @Transient
- public boolean isInfraGeneric() {
- if (rank == null){
- return false;
- }
- return getRank().isInfraGeneric();
- }
- /**
- * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
- * taxon name is the species rank (true) or not (false). Non viral names
- * with species rank are binomials.
- * Returns false if rank is null.
- *
- * @see #isSupraGeneric()
- * @see #isGenus()
- * @see #isInfraGeneric()
- * @see #isInfraSpecific()
- */
- @Transient
- public boolean isSpecies() {
- if (rank == null){
- return false;
- }
- return getRank().isSpecies();
- }
- /**
- * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
- * taxon name is lower than the species rank (true) or not (false).
- * Infraspecific non viral names are trinomials.
- * Returns false if rank is null.
- *
- * @see #isSupraGeneric()
- * @see #isGenus()
- * @see #isInfraGeneric()
- * @see #isSpecies()
- */
- @Transient
- public boolean isInfraSpecific() {
- if (rank == null){
- return false;
- }
- return getRank().isInfraSpecific();
- }
-
-
- /**
- * Returns null as the {@link NomenclaturalCode nomenclatural code} that governs
- * the construction of <i>this</i> taxon name since there is no specific
- * nomenclatural code defined. The real implementention takes place in the
- * subclasses {@link ViralName ViralName}, {@link BacterialName BacterialName},
- * {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName} and
- * {@link ZoologicalName ZoologicalName}. Each taxon name is governed by one
- * and only one nomenclatural code.
- *
- * @return null
- * @see #isCodeCompliant()
- * @see #getHasProblem()
- */
- @Transient
- abstract public NomenclaturalCode getNomenclaturalCode();
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
- */
- /**
- * Generates and returns the string with the scientific name of <i>this</i>
- * taxon name (only non viral taxon names can be generated from their
- * components). This string may be stored in the inherited
- * {@link common.IdentifiableEntity#getTitleCache() titleCache} attribute.
- * This method overrides the generic and inherited
- * IdentifiableEntity#generateTitle() method.
- *
- * @return the string with the composed name of this non viral taxon name with authorship (and maybe year)
- * @see common.IdentifiableEntity#generateTitle()
- * @see common.IdentifiableEntity#getTitleCache()
- */
- @Override
- public String generateTitle() {
- // TODO Auto-generated method stub
- logger.warn("not yet implemented");
- return null;
- }
-
-}
\ No newline at end of file
+ /**
+ * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
+ * taxon name is higher than the genus rank (true) or not (false).
+ * Suprageneric non viral names are monomials.
+ * Returns false if rank is null.
+ *
+ * @see #isGenus()
+ * @see #isInfraGeneric()
+ * @see #isSpecies()
+ * @see #isInfraSpecific()
+ */
+ @Transient
+ public boolean isSupraGeneric() {
+ if (rank == null){
+ return false;
+ }
+ return getRank().isSupraGeneric();
+ }
+ /**
+ * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
+ * taxon name is the genus rank (true) or not (false). Non viral names with
+ * genus rank are monomials. Returns false if rank is null.
+ *
+ * @see #isSupraGeneric()
+ * @see #isInfraGeneric()
+ * @see #isSpecies()
+ * @see #isInfraSpecific()
+ */
+ @Transient
+ public boolean isGenus() {
+ if (rank == null){
+ return false;
+ }
+ return getRank().isGenus();
+ }
+ /**
+ * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
+ * taxon name is higher than the species rank and lower than the
+ * genus rank (true) or not (false). Infrageneric non viral names are
+ * binomials. Returns false if rank is null.
+ *
+ * @see #isSupraGeneric()
+ * @see #isGenus()
+ * @see #isSpecies()
+ * @see #isInfraSpecific()
+ */
+ @Transient
+ public boolean isInfraGeneric() {
+ if (rank == null){
+ return false;
+ }
+ return getRank().isInfraGeneric();
+ }
+
+ /**
+ * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
+ * taxon name is higher than the species rank (true) or not (false).
+ * Returns false if rank is null.
+ *
+ * @see #isGenus()
+ * @see #isInfraGeneric()
+ * @see #isSpecies()
+ * @see #isInfraSpecific()
+ */
+ @Transient
+ public boolean isSupraSpecific(){
+ if (rank == null) {
+ return false;
+ }
+ return getRank().isHigher(Rank.SPECIES());
+ }
+
+ /**
+ * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
+ * taxon name is the species rank (true) or not (false). Non viral names
+ * with species rank are binomials.
+ * Returns false if rank is null.
+ *
+ * @see #isSupraGeneric()
+ * @see #isGenus()
+ * @see #isInfraGeneric()
+ * @see #isInfraSpecific()
+ */
+ @Transient
+ public boolean isSpecies() {
+ if (rank == null){
+ return false;
+ }
+ return getRank().isSpecies();
+ }
+ /**
+ * Returns the boolean value indicating whether the taxonomic {@link Rank rank} of <i>this</i>
+ * taxon name is lower than the species rank (true) or not (false).
+ * Infraspecific non viral names are trinomials.
+ * Returns false if rank is null.
+ *
+ * @see #isSupraGeneric()
+ * @see #isGenus()
+ * @see #isInfraGeneric()
+ * @see #isSpecies()
+ */
+ @Transient
+ public boolean isInfraSpecific() {
+ if (rank == null){
+ return false;
+ }
+ return getRank().isInfraSpecific();
+ }
+
+
+ /**
+ * Returns null as the {@link NomenclaturalCode nomenclatural code} that governs
+ * the construction of <i>this</i> taxon name since there is no specific
+ * nomenclatural code defined. The real implementention takes place in the
+ * subclasses {@link ViralName ViralName}, {@link BacterialName BacterialName},
+ * {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName} and
+ * {@link ZoologicalName ZoologicalName}. Each taxon name is governed by one
+ * and only one nomenclatural code.
+ *
+ * @return null
+ * @see #isCodeCompliant()
+ * @see #getHasProblem()
+ */
+ abstract public NomenclaturalCode getNomenclaturalCode();
+
+ /* (non-Javadoc)
+ * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
+ */
+ /**
+ * Generates and returns the string with the scientific name of <i>this</i>
+ * taxon name (only non viral taxon names can be generated from their
+ * components). This string may be stored in the inherited
+ * {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache() titleCache} attribute.
+ * This method overrides the generic and inherited
+ * {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle() method} from
+ * {@link eu.etaxonomy.cdm.model.common.IdentifiableEntity IdentifiableEntity}.
+ *
+ * @return the string with the composed name of this non viral taxon name with authorship (and maybe year)
+ * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#generateTitle()
+ * @see eu.etaxonomy.cdm.model.common.IdentifiableEntity#getTitleCache()
+ */
+// @Override
+// public abstract String generateTitle();
+
+ /**
+ * Creates a basionym relationship between this name and
+ * each name in its homotypic group.
+ *
+ * @param basionymName
+ */
+ @Transient
+ public void setAsGroupsBasionym() {
+
+
+ HomotypicalGroup homotypicalGroup = this.getHomotypicalGroup();
+
+ if (homotypicalGroup == null) {
+ return;
+ }
+
+ Set<NameRelationship> relations = new HashSet<NameRelationship>();
+ Set<NameRelationship> removeRelations = new HashSet<NameRelationship>();
+
+ for(TaxonNameBase<?, ?> typifiedName : homotypicalGroup.getTypifiedNames()){
+
+ Set<NameRelationship> nameRelations = typifiedName.getRelationsFromThisName();
+
+ for(NameRelationship nameRelation : nameRelations){
+ relations.add(nameRelation);
+ }
+ }
+
+ for (NameRelationship relation : relations) {
+
+ // If this is a basionym relation, and toName is in the homotypical group,
+ // remove the relationship.
+ if (relation.getType().equals(NameRelationshipType.BASIONYM()) &&
+ relation.getToName().getHomotypicalGroup().equals(homotypicalGroup)) {
+ removeRelations.add(relation);
+ }
+ }
+
+ // Removing relations from a set through which we are iterating causes a
+ // ConcurrentModificationException. Therefore, we delete the targeted
+ // relations in a second step.
+ for (NameRelationship relation : removeRelations) {
+ this.removeNameRelationship(relation);
+ }
+
+
+ for (TaxonNameBase<?, ?> name : homotypicalGroup.getTypifiedNames()) {
+ if (!name.equals(this)) {
+
+ // First check whether the relationship already exists
+ if (!this.isBasionymFor(name)) {
+
+ // Then create it
+ name.addRelationshipFromName(this,
+ NameRelationshipType.BASIONYM(), null);
+ }
+ }
+ }
+ }
+
+ /**
+ * Removes basionym relationship between this name and
+ * each name in its homotypic group.
+ *
+ * @param basionymName
+ */
+ @Transient
+ public void removeAsGroupsBasionym() {
+
+ HomotypicalGroup homotypicalGroup = this.getHomotypicalGroup();
+
+ if (homotypicalGroup == null) {
+ return;
+ }
+
+ Set<NameRelationship> relations = new HashSet<NameRelationship>();
+ Set<NameRelationship> removeRelations = new HashSet<NameRelationship>();
+
+ for(TaxonNameBase<?, ?> typifiedName : homotypicalGroup.getTypifiedNames()){
+
+ Set<NameRelationship> nameRelations = typifiedName.getRelationsFromThisName();
+
+ for(NameRelationship nameRelation : nameRelations){
+ relations.add(nameRelation);
+ }
+ }
+
+ for (NameRelationship relation : relations) {
+
+ // If this is a basionym relation, and toName is in the homotypical group,
+ // and fromName is basionymName, remove the relationship.
+ if (relation.getType().equals(NameRelationshipType.BASIONYM()) &&
+ relation.getFromName().equals(this) &&
+ relation.getToName().getHomotypicalGroup().equals(homotypicalGroup)) {
+ removeRelations.add(relation);
+ }
+ }
+
+ // Removing relations from a set through which we are iterating causes a
+ // ConcurrentModificationException. Therefore, we delete the targeted
+ // relations in a second step.
+ for (NameRelationship relation : removeRelations) {
+ this.removeNameRelationship(relation);
+ }
+ }
+
+//*********************** CLONE ********************************************************/
+
+ /**
+ * Clones <i>this</i> taxon name. This is a shortcut that enables to create
+ * a new instance that differs only slightly from <i>this</i> taxon name by
+ * modifying only some of the attributes.<BR><BR>
+ * Usages of this name in a taxon concept are <b>not</b> cloned.<BR>
+ * <b>The name gets a newly created homotypical group</b><BR>
+ * (CAUTION: this behaviour needs to be discussed and may change in future).<BR><BR>
+ * {@link TaxonNameDescription Name descriptions} are cloned and not reused.<BR>
+ * {@link TypeDesignationBase Type designations} are cloned and not reused.<BR>
+ *
+ * @see eu.etaxonomy.cdm.model.media.IdentifiableEntity#clone()
+ * @see java.lang.Object#clone()
+ */
+ @Override
+ public Object clone() {
+ TaxonNameBase result;
+ try {
+ result = (TaxonNameBase)super.clone();
+
+ //taxonBases -> empty
+ result.taxonBases = new HashSet<TaxonBase>();
+
+ //empty caches
+ if (! protectedFullTitleCache){
+ result.fullTitleCache = null;
+ }
+
+ //descriptions
+ result.descriptions = new HashSet<TaxonNameDescription>();
+ for (TaxonNameDescription taxonNameDescription : getDescriptions()){
+ TaxonNameDescription newDescription = (TaxonNameDescription)taxonNameDescription.clone();
+ result.descriptions.add(newDescription);
+ }
+
+ //status
+ result.status = new HashSet<NomenclaturalStatus>();
+ for (NomenclaturalStatus nomenclaturalStatus : getStatus()){
+ NomenclaturalStatus newStatus = (NomenclaturalStatus)nomenclaturalStatus.clone();
+ result.status.add(newStatus);
+ }
+
+
+ //To Relations
+ result.relationsToThisName = new HashSet<NameRelationship>();
+ for (NameRelationship toRelationship : getRelationsToThisName()){
+ NameRelationship newRelationship = (NameRelationship)toRelationship.clone();
+ newRelationship.setRelatedTo(result);
+ result.relationsToThisName.add(newRelationship);
+ }
+
+ //From Relations
+ result.relationsFromThisName = new HashSet<NameRelationship>();
+ for (NameRelationship fromRelationship : getRelationsFromThisName()){
+ NameRelationship newRelationship = (NameRelationship)fromRelationship.clone();
+ newRelationship.setRelatedFrom(result);
+ result.relationsFromThisName.add(newRelationship);
+ }
+
+ //type designations
+ result.typeDesignations = new HashSet<TypeDesignationBase>();
+ for (TypeDesignationBase typeDesignation : getTypeDesignations()){
+ TypeDesignationBase newDesignation = (TypeDesignationBase)typeDesignation.clone();
+ result.typeDesignations.add(newDesignation);
+ newDesignation.addTypifiedName(result);
+ }
+
+ //homotypicalGroup
+ //TODO still needs to be discussed
+ homotypicalGroup = HomotypicalGroup.NewInstance();
+ homotypicalGroup.addTypifiedName(this);
+
+ //no changes to: appendedPharse, nomenclaturalReference,
+ //nomenclaturalMicroReference, parsingProblem, problemEnds, problemStarts
+ //protectedFullTitleCache, rank
+ return result;
+ } catch (CloneNotSupportedException e) {
+ logger.warn("Object does not implement cloneable");
+ e.printStackTrace();
+ return null;
+ }
+
+ }
+}
BGBM BDI Projects / cdmlib.git / blobdiff