package eu.etaxonomy.cdm.model.name;
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.Transient;
-import javax.validation.constraints.NotNull;
-import javax.validation.constraints.Pattern;
-import javax.validation.constraints.Size;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
-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.XmlType;
-import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
import org.hibernate.envers.Audited;
-import org.hibernate.search.annotations.Analyze;
-import org.hibernate.search.annotations.Analyzer;
-import org.hibernate.search.annotations.Field;
-import org.hibernate.search.annotations.Fields;
-import org.hibernate.search.annotations.Index;
import org.hibernate.search.annotations.Indexed;
-import org.hibernate.search.annotations.IndexedEmbedded;
-import org.hibernate.search.annotations.Store;
-import org.hibernate.validator.constraints.NotEmpty;
import org.springframework.beans.factory.annotation.Configurable;
-import eu.etaxonomy.cdm.common.CdmUtils;
-import eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor;
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
-import eu.etaxonomy.cdm.model.common.CdmBase;
-import eu.etaxonomy.cdm.model.common.RelationshipBase;
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
-import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.strategy.cache.name.CacheUpdate;
import eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy;
-import eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy;
-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.validation.Level2;
import eu.etaxonomy.cdm.validation.Level3;
import eu.etaxonomy.cdm.validation.annotation.CorrectEpithetsForRank;
import eu.etaxonomy.cdm.validation.annotation.NameMustHaveAuthority;
import eu.etaxonomy.cdm.validation.annotation.NoDuplicateNames;
-import eu.etaxonomy.cdm.validation.annotation.NullOrNotEmpty;
/**
* The taxon name class for all non viral taxa. Parenthetical authorship is derived
* </ul>
*
* @author m.doering
- * @version 1.0
* @created 08-Nov-2007 13:06:39
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "NonViralName", propOrder = {
- "nameCache",
- "genusOrUninomial",
- "infraGenericEpithet",
- "specificEpithet",
- "infraSpecificEpithet",
- "combinationAuthorTeam",
- "exCombinationAuthorTeam",
- "basionymAuthorTeam",
- "exBasionymAuthorTeam",
- "authorshipCache",
- "protectedAuthorshipCache",
- "protectedNameCache",
- "hybridParentRelations",
- "hybridChildRelations",
- "hybridFormula",
- "monomHybrid",
- "binomHybrid",
- "trinomHybrid"
-})
+@XmlType(name = "NonViralName", propOrder = {})
@XmlRootElement(name = "NonViralName")
@Entity
@Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")
@Audited
@Configurable
+
@CorrectEpithetsForRank(groups = Level2.class)
@NameMustHaveAuthority(groups = Level2.class)
@NoDuplicateNames(groups = Level3.class)
-public class NonViralName<T extends NonViralName> extends TaxonNameBase<T, INonViralNameCacheStrategy> implements Cloneable{
- private static final long serialVersionUID = 4441110073881088033L;
- private static final Logger logger = Logger.getLogger(NonViralName.class);
-
- @XmlElement(name = "NameCache")
- @Fields({
- @Field(name = "nameCache_tokenized"),
- @Field(store = Store.YES, index = Index.YES, analyze = Analyze.YES)
- })
- @Analyzer (impl = org.apache.lucene.analysis.KeywordAnalyzer.class)
- @Match(value=MatchMode.CACHE, cacheReplaceMode=ReplaceMode.DEFINED,
- cacheReplacedProperties={"genusOrUninomial", "infraGenericEpithet", "specificEpithet", "infraSpecificEpithet"} )
- @NotEmpty(groups = Level2.class) // implicitly NotNull
- @Size(max = 255)
- private String nameCache;
-
- @XmlElement(name = "ProtectedNameCache")
- @CacheUpdate(value="nameCache")
- protected boolean protectedNameCache;
-
- @XmlElement(name = "GenusOrUninomial")
- @Field(analyze = Analyze.YES,indexNullAs=Field.DEFAULT_NULL_TOKEN)
- @Match(MatchMode.EQUAL_REQUIRED)
- @CacheUpdate("nameCache")
- @Size(max = 255)
- @Pattern(regexp = "[A-Z][a-z\\u00E4\\u00EB\\u00EF\\u00F6\\u00FC\\-]+", groups=Level2.class, message="{eu.etaxonomy.cdm.model.name.NonViralName.allowedCharactersForUninomial.message}")
- @NullOrNotEmpty
- @NotNull(groups = Level2.class)
- private String genusOrUninomial;
-
- @XmlElement(name = "InfraGenericEpithet")
- @Field(analyze = Analyze.YES,indexNullAs=Field.DEFAULT_NULL_TOKEN)
- @CacheUpdate("nameCache")
- //TODO Val #3379
-// @NullOrNotEmpty
- @Size(max = 255)
- @Pattern(regexp = "[a-z\\u00E4\\u00EB\\u00EF\\u00F6\\u00FC\\-]+", groups=Level2.class,message="{eu.etaxonomy.cdm.model.name.NonViralName.allowedCharactersForEpithet.message}")
- private String infraGenericEpithet;
-
- @XmlElement(name = "SpecificEpithet")
- @Field(analyze = Analyze.YES,indexNullAs=Field.DEFAULT_NULL_TOKEN)
- @CacheUpdate("nameCache")
- //TODO Val #3379
-// @NullOrNotEmpty
- @Size(max = 255)
- @Pattern(regexp = "[a-z\\u00E4\\u00EB\\u00EF\\u00F6\\u00FC\\-]+", groups=Level2.class, message = "{eu.etaxonomy.cdm.model.name.NonViralName.allowedCharactersForEpithet.message}")
- private String specificEpithet;
-
- @XmlElement(name = "InfraSpecificEpithet")
- @Field(analyze = Analyze.YES,indexNullAs=Field.DEFAULT_NULL_TOKEN)
- @CacheUpdate("nameCache")
- //TODO Val #3379
-// @NullOrNotEmpty
- @Size(max = 255)
- @Pattern(regexp = "[a-z\\u00E4\\u00EB\\u00EF\\u00F6\\u00FC\\-]+", groups=Level2.class, message = "{eu.etaxonomy.cdm.model.name.NonViralName.allowedCharactersForEpithet.message}")
- private String infraSpecificEpithet;
-
- @XmlElement(name = "CombinationAuthorTeam", type = TeamOrPersonBase.class)
- @XmlIDREF
- @XmlSchemaType(name = "IDREF")
- @ManyToOne(fetch = FetchType.LAZY)
-// @Target(TeamOrPersonBase.class)
- @Cascade(CascadeType.SAVE_UPDATE)
- @CacheUpdate("authorshipCache")
- @IndexedEmbedded
- private TeamOrPersonBase<?> combinationAuthorTeam;
-
- @XmlElement(name = "ExCombinationAuthorTeam", type = TeamOrPersonBase.class)
- @XmlIDREF
- @XmlSchemaType(name = "IDREF")
- @ManyToOne(fetch = FetchType.LAZY)
-// @Target(TeamOrPersonBase.class)
- @Cascade(CascadeType.SAVE_UPDATE)
- @CacheUpdate("authorshipCache")
- @IndexedEmbedded
- private TeamOrPersonBase<?> exCombinationAuthorTeam;
-
- @XmlElement(name = "BasionymAuthorTeam", type = TeamOrPersonBase.class)
- @XmlIDREF
- @XmlSchemaType(name = "IDREF")
- @ManyToOne(fetch = FetchType.LAZY)
-// @Target(TeamOrPersonBase.class)
- @Cascade(CascadeType.SAVE_UPDATE)
- @CacheUpdate("authorshipCache")
- @IndexedEmbedded
- private TeamOrPersonBase<?> basionymAuthorTeam;
-
- @XmlElement(name = "ExBasionymAuthorTeam", type = TeamOrPersonBase.class)
- @XmlIDREF
- @XmlSchemaType(name = "IDREF")
- @ManyToOne(fetch = FetchType.LAZY)
-// @Target(TeamOrPersonBase.class)
- @Cascade(CascadeType.SAVE_UPDATE)
- @CacheUpdate("authorshipCache")
- @IndexedEmbedded
- private TeamOrPersonBase<?> exBasionymAuthorTeam;
-
- @XmlElement(name = "AuthorshipCache")
- @Fields({
- @Field(name = "authorshipCache_tokenized"),
- @Field(analyze = Analyze.NO)
- })
- @Match(value=MatchMode.CACHE, cacheReplaceMode=ReplaceMode.DEFINED,
- cacheReplacedProperties={"combinationAuthorTeam", "basionymAuthorTeam", "exCombinationAuthorTeam", "exBasionymAuthorTeam"} )
- //TODO Val #3379
-// @NotNull
- @Size(max = 255)
- @Pattern(regexp = "^[A-Za-z0-9 \\u00E4\\u00EB\\u00EF\\u00F6\\u00FC\\-\\&\\,\\(\\)\\.]+$", groups=Level2.class, message = "{eu.etaxonomy.cdm.model.name.NonViralName.allowedCharactersForAuthority.message}")
- private String authorshipCache;
+public class NonViralName<T extends NonViralName<?>>
+ extends TaxonNameBase<T, INonViralNameCacheStrategy<T>>{
- @XmlElement(name = "ProtectedAuthorshipCache")
- @CacheUpdate("authorshipCache")
- protected boolean protectedAuthorshipCache;
-
- @XmlElementWrapper(name = "HybridRelationsFromThisName")
- @XmlElement(name = "HybridRelationsFromThisName")
- @OneToMany(mappedBy="relatedFrom", fetch = FetchType.LAZY)
- @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
- @Merge(MergeMode.RELATION)
- @NotNull
- private Set<HybridRelationship> hybridParentRelations = new HashSet<HybridRelationship>();
-
- @XmlElementWrapper(name = "HybridRelationsToThisName")
- @XmlElement(name = "HybridRelationsToThisName")
- @OneToMany(mappedBy="relatedTo", fetch = FetchType.LAZY, orphanRemoval=true) //a hybrid relation can be deleted automatically if the child is deleted.
- @Cascade({CascadeType.SAVE_UPDATE, CascadeType.MERGE, CascadeType.DELETE})
- @Merge(MergeMode.RELATION)
- @NotNull
- private Set<HybridRelationship> hybridChildRelations = new HashSet<HybridRelationship>();
-
- //if set: this name is a hybrid formula (a hybrid that does not have an own name) and no other hybrid flags may be set. A
- //hybrid name may not have either an authorteam nor other name components.
- @XmlElement(name ="IsHybridFormula")
- @CacheUpdate("nameCache")
- private boolean hybridFormula = false;
-
- @XmlElement(name ="IsMonomHybrid")
- @CacheUpdate("nameCache")
- private boolean monomHybrid = false;
-
- @XmlElement(name ="IsBinomHybrid")
- @CacheUpdate("nameCache")
- private boolean binomHybrid = false;
-
- @XmlElement(name ="IsTrinomHybrid")
- @CacheUpdate("nameCache")
- private boolean trinomHybrid = false;
-
- /**
- * Creates a new non viral taxon name instance
- * only containing its {@link common.Rank rank} and
- * the {@link eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy default cache strategy}.
- *
- * @param rank the rank to be assigned to <i>this</i> non viral taxon name
- * @see #NewInstance(Rank, HomotypicalGroup)
- * @see #NonViralName(Rank, HomotypicalGroup)
- * @see #NonViralName()
- * @see #NonViralName(Rank, String, String, String, String, TeamOrPersonBase, Reference, String, HomotypicalGroup)
- * @see eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
- */
- public static NonViralName NewInstance(Rank rank){
- return new NonViralName(rank, null);
- }
-
- /**
- * Creates a new non viral taxon name instance
- * only containing its {@link common.Rank rank},
- * its {@link HomotypicalGroup homotypical group} and
- * the {@link eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy default cache strategy}.
- * The new non viral taxon name instance will be also added to the set of
- * non viral taxon names belonging to this homotypical group.
- *
- * @param rank the rank to be assigned to <i>this</i> non viral taxon name
- * @param homotypicalGroup the homotypical group to which <i>this</i> non viral taxon name belongs
- * @see #NewInstance(Rank)
- * @see #NonViralName(Rank, HomotypicalGroup)
- * @see #NonViralName()
- * @see #NonViralName(Rank, String, String, String, String, TeamOrPersonBase, Reference, String, HomotypicalGroup)
- * @see eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
- */
- public static NonViralName NewInstance(Rank rank, HomotypicalGroup homotypicalGroup){
- return new NonViralName(rank, homotypicalGroup);
- }
+ private static final long serialVersionUID = -9083811681449792683L;
// ************************** CONSTRUCTORS *************/
//needed by hibernate
- /**
- * Class constructor: creates a new non viral taxon name instance
- * only containing the {@link eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy default cache strategy}.
- *
- * @see #NonViralName(Rank, HomotypicalGroup)
- * @see #NonViralName(Rank, String, String, String, String, TeamOrPersonBase, Reference, String, HomotypicalGroup)
- * @see eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
- */
protected NonViralName(){
super();
- setNameCacheStrategy();
}
- /**
- * Class constructor: creates a new non viral taxon name instance
- * only containing its {@link Rank rank},
- * its {@link HomotypicalGroup homotypical group} and
- * the {@link eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy default cache strategy}.
- * The new non viral taxon name instance will be also added to the set of
- * non viral taxon names belonging to this homotypical group.
- *
- * @param rank the rank to be assigned to <i>this</i> non viral taxon name
- * @param homotypicalGroup the homotypical group to which <i>this</i> non viral taxon name belongs
- * @see #NonViralName()
- * @see #NonViralName(Rank, String, String, String, String, TeamOrPersonBase, Reference, String, HomotypicalGroup)
- * @see #NewInstance(Rank, HomotypicalGroup)
- * @see eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
- */
protected NonViralName(Rank rank, HomotypicalGroup homotypicalGroup) {
super(rank, homotypicalGroup);
- setNameCacheStrategy();
- }
- /**
- * Class constructor: creates a new non viral taxon name instance
- * containing its {@link Rank rank},
- * its {@link HomotypicalGroup homotypical group},
- * its scientific name components, its {@link eu.etaxonomy.cdm.model.agent.TeamOrPersonBase author(team)},
- * its {@link eu.etaxonomy.cdm.model.reference.Reference nomenclatural reference} and
- * the {@link eu.etaxonomy.cdm.strategy.cache.name.NonViralNameDefaultCacheStrategy default cache strategy}.
- * The new non viral taxon name instance will be also added to the set of
- * non viral taxon names belonging to this homotypical group.
- *
- * @param rank the rank to be assigned to <i>this</i> non viral taxon name
- * @param genusOrUninomial the string for <i>this</i> non viral taxon name
- * if its rank is genus or higher or for the genus part
- * if its rank is lower than genus
- * @param infraGenericEpithet the string for the first epithet of
- * <i>this</i> non viral taxon name if its rank is lower than genus
- * and higher than species aggregate
- * @param specificEpithet the string for the first epithet of
- * <i>this</i> non viral taxon name if its rank is species aggregate or lower
- * @param infraSpecificEpithet the string for the second epithet of
- * <i>this</i> non viral taxon name if its rank is lower than species
- * @param combinationAuthorTeam the author or the team who published <i>this</i> non viral taxon name
- * @param nomenclaturalReference the nomenclatural reference where <i>this</i> non viral taxon name was published
- * @param nomenclMicroRef the string with the details for precise location within the nomenclatural reference
- * @param homotypicalGroup the homotypical group to which <i>this</i> non viral taxon name belongs
- * @see #NonViralName()
- * @see #NonViralName(Rank, HomotypicalGroup)
- * @see #NewInstance(Rank, HomotypicalGroup)
- * @see eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
- */
- protected NonViralName(Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorTeam, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
- super(rank, homotypicalGroup);
- setNameCacheStrategy();
- setGenusOrUninomial(genusOrUninomial);
- setInfraGenericEpithet (infraGenericEpithet);
- setSpecificEpithet(specificEpithet);
- setInfraSpecificEpithet(infraSpecificEpithet);
- setCombinationAuthorTeam(combinationAuthorTeam);
- setNomenclaturalReference(nomenclaturalReference);
- this.setNomenclaturalMicroReference(nomenclMicroRef);
- }
-
-
-
-//**************************** METHODS **************************************/
-
-
- private void setNameCacheStrategy(){
- if (getClass() == NonViralName.class){
- this.cacheStrategy = NonViralNameDefaultCacheStrategy.NewInstance();
- }
- }
-
- @Override
- protected void initListener(){
- PropertyChangeListener listener = new PropertyChangeListener() {
- @Override
- public void propertyChange(PropertyChangeEvent e) {
- boolean protectedByLowerCache = false;
- //authorship cache
- if (fieldHasCacheUpdateProperty(e.getPropertyName(), "authorshipCache")){
- if (protectedAuthorshipCache){
- protectedByLowerCache = true;
- }else{
- authorshipCache = null;
- }
- }
-
- //nameCache
- if (fieldHasCacheUpdateProperty(e.getPropertyName(), "nameCache")){
- if (protectedNameCache){
- protectedByLowerCache = true;
- }else{
- nameCache = null;
- }
- }
- //title cache
- if (! fieldHasNoUpdateProperty(e.getPropertyName(), "titleCache")){
- if (isProtectedTitleCache()|| protectedByLowerCache == true ){
- protectedByLowerCache = true;
- }else{
- titleCache = null;
- }
- }
- //full title cache
- if (! fieldHasNoUpdateProperty(e.getPropertyName(), "fullTitleCache")){
- if (isProtectedFullTitleCache()|| protectedByLowerCache == true ){
- protectedByLowerCache = true;
- }else{
- fullTitleCache = null;
- }
- }
- }
- };
- addPropertyChangeListener(listener); //didn't use this.addXXX to make lsid.AssemblerTest run in cdmlib-remote
- }
-
- private static Map<String, java.lang.reflect.Field> allFields = null;
- @Override
- protected Map<String, java.lang.reflect.Field> getAllFields(){
- if (allFields == null){
- allFields = CdmUtils.getAllFields(this.getClass(), CdmBase.class, false, false, false, true);
- }
- return allFields;
- }
-
- /**
- * @param propertyName
- * @param string
- * @return
- */
- private boolean fieldHasCacheUpdateProperty(String propertyName, String cacheName) {
- java.lang.reflect.Field field;
- try {
- field = getAllFields().get(propertyName);
- if (field != null){
- CacheUpdate updateAnnotation = field.getAnnotation(CacheUpdate.class);
- if (updateAnnotation != null){
- for (String value : updateAnnotation.value()){
- if (cacheName.equals(value)){
- return true;
- }
- }
- }
- }
- return false;
- } catch (SecurityException e1) {
- throw e1;
- }
- }
-
- private boolean fieldHasNoUpdateProperty(String propertyName, String cacheName) {
- java.lang.reflect.Field field;
- //do not update fields with the same name
- if (cacheName.equals(propertyName)){
- return true;
- }
- //evaluate annotation
- try {
- field = getAllFields().get(propertyName);
- if (field != null){
- CacheUpdate updateAnnotation = field.getAnnotation(CacheUpdate.class);
- if (updateAnnotation != null){
- for (String value : updateAnnotation.noUpdate()){
- if (cacheName.equals(value)){
- return true;
- }
- }
- }
- }
- return false;
- } catch (SecurityException e1) {
- throw e1;
- }
- }
-
-
- /**
- * Returns the {@link eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor author (team)} that published <i>this</i> non viral
- * taxon name.
- *
- * @return the nomenclatural author (team) of <i>this</i> non viral taxon name
- * @see eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor
- * @see eu.etaxonomy.cdm.model.agent.TeamOrPersonBase#getNomenclaturalTitle()
- */
- public TeamOrPersonBase<?> getCombinationAuthorTeam(){
- return this.combinationAuthorTeam;
- }
-
- /**
- * @see #getCombinationAuthorTeam()
- */
- public void setCombinationAuthorTeam(TeamOrPersonBase<?> combinationAuthorTeam){
- this.combinationAuthorTeam = combinationAuthorTeam;
- }
-
- /**
- * Returns the {@link eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor author (team)} that contributed to
- * the publication of <i>this</i> non viral taxon name as generally stated by
- * the {@link #getCombinationAuthorTeam() combination author (team)} itself.<BR>
- * An ex-author(-team) is an author(-team) to whom a taxon name was ascribed
- * although it is not the author(-team) of a valid publication (for instance
- * without the validating description or diagnosis in case of a name for a
- * new taxon). The name of this ascribed authorship, followed by "ex", may
- * be inserted before the name(s) of the publishing author(s) of the validly
- * published name:<BR>
- * <i>Lilium tianschanicum</i> was described by Grubov (1977) as a new species and
- * its name was ascribed to Ivanova; since there is no indication that
- * Ivanova provided the validating description, the name may be cited as
- * <i>Lilium tianschanicum</i> N. A. Ivanova ex Grubov or <i>Lilium tianschanicum</i> Grubov.
- * <P>
- * The presence of an author (team) of <i>this</i> non viral taxon name is a
- * condition for the existence of an ex author (team) for <i>this</i> same name.
- *
- * @return the nomenclatural ex author (team) of <i>this</i> non viral taxon name
- * @see #getCombinationAuthorTeam()
- * @see eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor
- * @see eu.etaxonomy.cdm.model.agent.TeamOrPersonBase#getNomenclaturalTitle()
- */
- public TeamOrPersonBase<?> getExCombinationAuthorTeam(){
- return this.exCombinationAuthorTeam;
- }
-
- /**
- * @see #getExCombinationAuthorTeam()
- */
- public void setExCombinationAuthorTeam(TeamOrPersonBase<?> exCombinationAuthorTeam){
- this.exCombinationAuthorTeam = exCombinationAuthorTeam;
- }
-
- /**
- * Returns the {@link eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor author (team)} that published the original combination
- * on which <i>this</i> non viral taxon name is nomenclaturally based. Such an
- * author (team) can only exist if <i>this</i> non viral taxon name is a new
- * combination due to a taxonomical revision.
- *
- * @return the nomenclatural basionym author (team) of <i>this</i> non viral taxon name
- * @see #getCombinationAuthorTeam()
- * @see eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor
- * @see eu.etaxonomy.cdm.model.agent.TeamOrPersonBase#getNomenclaturalTitle()
- */
- public TeamOrPersonBase<?> getBasionymAuthorTeam(){
- return basionymAuthorTeam;
- }
-
- /**
- * @see #getBasionymAuthorTeam()
- */
- public void setBasionymAuthorTeam(TeamOrPersonBase<?> basionymAuthorTeam) {
- this.basionymAuthorTeam = basionymAuthorTeam;
- }
-
- /**
- * Returns the {@link eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor author (team)} that contributed to
- * the publication of the original combination <i>this</i> non viral taxon name is
- * based on. This should have been generally stated by
- * the {@link #getBasionymAuthorTeam() basionym author (team)} itself.
- * The presence of a basionym author (team) of <i>this</i> non viral taxon name is a
- * condition for the existence of an ex basionym author (team)
- * for <i>this</i> same name.
- *
- * @return the nomenclatural ex basionym author (team) of <i>this</i> non viral taxon name
- * @see #getBasionymAuthorTeam()
- * @see #getExCombinationAuthorTeam()
- * @see #getCombinationAuthorTeam()
- * @see eu.etaxonomy.cdm.model.agent.INomenclaturalAuthor
- * @see eu.etaxonomy.cdm.model.agent.TeamOrPersonBase#getNomenclaturalTitle()
- */
- public TeamOrPersonBase<?> getExBasionymAuthorTeam(){
- return exBasionymAuthorTeam;
- }
-
- /**
- * @see #getExBasionymAuthorTeam()
- */
- public void setExBasionymAuthorTeam(TeamOrPersonBase<?> exBasionymAuthorTeam) {
- this.exBasionymAuthorTeam = exBasionymAuthorTeam;
- }
- /**
- * Returns either the scientific name string (without authorship) for <i>this</i>
- * non viral taxon name if its rank is genus or higher (monomial) or the string for
- * the genus part of it if its {@link Rank rank} is lower than genus (bi- or trinomial).
- * Genus or uninomial strings begin with an upper case letter.
- *
- * @return the string containing the suprageneric name, the genus name or the genus part of <i>this</i> non viral taxon name
- * @see #getNameCache()
- */
- public String getGenusOrUninomial() {
- return genusOrUninomial;
- }
-
- /**
- * @see #getGenusOrUninomial()
- */
- public void setGenusOrUninomial(String genusOrUninomial) {
- this.genusOrUninomial = StringUtils.isBlank(genusOrUninomial) ? null : genusOrUninomial;
- }
-
- /**
- * Returns the genus subdivision epithet string (infrageneric part) for
- * <i>this</i> non viral taxon name if its {@link Rank rank} is infrageneric (lower than genus and
- * higher than species aggregate: binomial). Genus subdivision epithet
- * strings begin with an upper case letter.
- *
- * @return the string containing the infrageneric part of <i>this</i> non viral taxon name
- * @see #getNameCache()
- */
- public String getInfraGenericEpithet(){
- return this.infraGenericEpithet;
- }
-
- /**
- * @see #getInfraGenericEpithet()
- */
- public void setInfraGenericEpithet(String infraGenericEpithet){
- this.infraGenericEpithet = StringUtils.isBlank(infraGenericEpithet)? null : infraGenericEpithet;
- }
-
- /**
- * Returns the species epithet string for <i>this</i> non viral taxon name if its {@link Rank rank} is
- * species aggregate or lower (bi- or trinomial). Species epithet strings
- * begin with a lower case letter.
- *
- * @return the string containing the species epithet of <i>this</i> non viral taxon name
- * @see #getNameCache()
- */
- public String getSpecificEpithet(){
- return this.specificEpithet;
- }
-
- /**
- * @see #getSpecificEpithet()
- */
- public void setSpecificEpithet(String specificEpithet){
- this.specificEpithet = StringUtils.isBlank(specificEpithet) ? null : specificEpithet;
- }
-
- /**
- * Returns the species subdivision epithet string (infraspecific part) for
- * <i>this</i> non viral taxon name if its {@link Rank rank} is infraspecific
- * (lower than species: trinomial). Species subdivision epithet strings
- * begin with a lower case letter.
- *
- * @return the string containing the infraspecific part of <i>this</i> non viral taxon name
- * @see #getNameCache()
- */
- public String getInfraSpecificEpithet(){
- return this.infraSpecificEpithet;
- }
-
- /**
- * @see #getInfraSpecificEpithet()
- */
- public void setInfraSpecificEpithet(String infraSpecificEpithet){
- this.infraSpecificEpithet = StringUtils.isBlank(infraSpecificEpithet)?null : infraSpecificEpithet;
- }
-
- /**
- * Generates and returns the string with the scientific name of <i>this</i>
- * non viral taxon name including author strings and maybe year according to
- * the strategy defined in
- * {@link eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy INonViralNameCacheStrategy}.
- * 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
- * TaxonNameBase#generateTitle() method.
- *
- * @return the string with the composed name of <i>this</i> 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()
- * @see TaxonNameBase#generateTitle()
- */
-// @Override
-// public String generateTitle(){
-// if (cacheStrategy == null){
-// logger.warn("No CacheStrategy defined for nonViralName: " + this.getUuid());
-// return null;
-// }else{
-// return cacheStrategy.getTitleCache(this);
-// }
-// }
-
- @Override
- public String generateFullTitle(){
- if (cacheStrategy == null){
- logger.warn("No CacheStrategy defined for nonViralName: " + this.getUuid());
- return null;
- }else{
- return cacheStrategy.getFullTitleCache(this);
- }
- }
-
- /**
- * Generates the composed name string of <i>this</i> non viral taxon name without author
- * strings or year according to the strategy defined in
- * {@link eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy INonViralNameCacheStrategy}.
- * The result might be stored in {@link #getNameCache() nameCache} if the
- * flag {@link #isProtectedNameCache() protectedNameCache} is not set.
- *
- * @return the string with the composed name of <i>this</i> non viral taxon name without authors or year
- * @see #getNameCache()
- */
- protected String generateNameCache(){
- if (cacheStrategy == null){
- logger.warn("No CacheStrategy defined for taxonName: " + this.toString());
- return null;
- }else{
- return cacheStrategy.getNameCache(this);
- }
- }
-
- /**
- * Returns or generates the nameCache (scientific name
- * without author strings and year) string for <i>this</i> non viral taxon name. If the
- * {@link #isProtectedNameCache() protectedNameCache} flag is not set (False)
- * the string will be generated according to a defined strategy,
- * otherwise the value of the actual nameCache string will be returned.
- *
- * @return the string which identifies <i>this</i> non viral taxon name (without authors or year)
- * @see #generateNameCache()
- */
- @Transient
- public String getNameCache() {
- if (protectedNameCache){
- return this.nameCache;
- }
- // is title dirty, i.e. equal NULL?
- if (nameCache == null){
- this.nameCache = generateNameCache();
- }
- return nameCache;
- }
-
- /**
- * Assigns a nameCache string to <i>this</i> non viral taxon name and protects it from being overwritten.
- * Sets the protectedNameCache flag to <code>true</code>.
- *
- * @param nameCache the string which identifies <i>this</i> non viral taxon name (without authors or year)
- * @see #getNameCache()
- */
- public void setNameCache(String nameCache){
- setNameCache(nameCache, true);
- }
-
- /**
- * Assigns a nameCache string to <i>this</i> non viral taxon name and protects it from being overwritten.
- * Sets the protectedNameCache flag to <code>true</code>.
- *
- * @param nameCache the string which identifies <i>this</i> non viral taxon name (without authors or year)
- * @param protectedNameCache if true teh protectedNameCache is set to <code>true</code> or otherwise set to
- * <code>false</code>
- * @see #getNameCache()
- */
- public void setNameCache(String nameCache, boolean protectedNameCache){
- this.nameCache = nameCache;
- this.setProtectedNameCache(protectedNameCache);
- }
-
- /**
- * Returns the boolean value of the flag intended to protect (true)
- * or not (false) the {@link #getNameCache() nameCache} (scientific name without author strings and year)
- * string of <i>this</i> non viral taxon name.
- *
- * @return the boolean value of the protectedNameCache flag
- * @see #getNameCache()
- */
- public boolean isProtectedNameCache() {
- return protectedNameCache;
- }
-
- /**
- * @see #isProtectedNameCache()
- */
- public void setProtectedNameCache(boolean protectedNameCache) {
- this.protectedNameCache = protectedNameCache;
- }
-
-
- /**
- * Generates and returns a concatenated and formated authorteams string
- * including basionym and combination authors of <i>this</i> non viral taxon name
- * according to the strategy defined in
- * {@link eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy#getAuthorshipCache(NonViralName) INonViralNameCacheStrategy}.
- *
- * @return the string with the concatenated and formated authorteams for <i>this</i> non viral taxon name
- * @see eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy#getAuthorshipCache(NonViralName)
- */
- public String generateAuthorship(){
- if (cacheStrategy == null){
- logger.warn("No CacheStrategy defined for nonViralName: " + this.getUuid());
- return null;
- }else{
- return ((INonViralNameCacheStrategy<T>)cacheStrategy).getAuthorshipCache((T)this);
- }
- }
-
- /**
- * Returns the concatenated and formated authorteams string including
- * basionym and combination authors of <i>this</i> non viral taxon name.
- * If the protectedAuthorshipCache flag is set this method returns the
- * string stored in the the authorshipCache attribute, otherwise it
- * generates the complete authorship string, returns it and stores it in
- * the authorshipCache attribute.
- *
- * @return the string with the concatenated and formated authorteams for <i>this</i> non viral taxon name
- * @see #generateAuthorship()
- */
- @Transient
- public String getAuthorshipCache() {
- if (protectedAuthorshipCache){
- return this.authorshipCache;
- }
- if (this.authorshipCache == null ){
- this.authorshipCache = generateAuthorship();
- }else{
- //TODO get is Dirty of authors, make better if possible
- this.setAuthorshipCache(generateAuthorship(), protectedAuthorshipCache); //throw change event to inform higher caches
-
- }
- return authorshipCache;
- }
-
-
- /**
- * Updates the authorship cache if any changes appeared in the authors nomenclatural caches.
- * Deletes the titleCache and the fullTitleCache if not protected and if any change has happened
- * @return
- */
- private void updateAuthorshipCache() {
- //updates the authorship cache if necessary and via the listener updates all higher caches
- if (protectedAuthorshipCache == false){
- String oldCache = this.authorshipCache;
- String newCache = this.getAuthorshipCache();
- if ( (oldCache == null && newCache != null) || CdmUtils.nullSafeEqual(oldCache,newCache)){
- this.setAuthorshipCache(this.getAuthorshipCache(), false);
- }
- }
- }
-
- /**
- * Assigns an authorshipCache string to <i>this</i> non viral taxon name. Sets the isProtectedAuthorshipCache
- * flag to <code>true</code>.
- *
- * @param authorshipCache the string which identifies the complete authorship of <i>this</i> non viral taxon name
- * @see #getAuthorshipCache()
- */
- public void setAuthorshipCache(String authorshipCache) {
- setAuthorshipCache(authorshipCache, true);
- }
-
- @Override
- @Transient
- public String getFullTitleCache(){
- updateAuthorshipCache();
- return super.getFullTitleCache();
- }
-
- @Override
- public String getTitleCache(){
- if(!protectedTitleCache) {
- updateAuthorshipCache();
- }
-
- return super.getTitleCache();
- }
-
-
- /**
- * Assigns an authorshipCache string to <i>this</i> non viral taxon name.
- *
- * @param authorshipCache the string which identifies the complete authorship of <i>this</i> non viral taxon name
- * @param protectedAuthorshipCache if true the isProtectedAuthorshipCache flag is set to <code>true</code>, otherwise
- * the flag is set to <code>false</code>.
- * @see #getAuthorshipCache()
- */
- public void setAuthorshipCache(String authorshipCache, boolean protectedAuthorshipCache) {
- this.authorshipCache = authorshipCache;
- this.setProtectedAuthorshipCache(protectedAuthorshipCache);
- }
-
- @Override
- public void setTitleCache(String titleCache, boolean protectCache){
- super.setTitleCache(titleCache, protectCache);
- }
-
- /**
- * 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} or
- * {@link ZoologicalName ZoologicalName} to which <i>this</i> non viral taxon name belongs.
- * This method overrides the isCodeCompliant method from the abstract
- * {@link TaxonNameBase#isCodeCompliant() TaxonNameBase} class.
- *
- * @return false
- * @see TaxonNameBase#isCodeCompliant()
- */
- @Override
- @Transient
- public boolean isCodeCompliant() {
- //FIXME
- logger.warn("is CodeCompliant not yet implemented");
- return false;
- }
-
-
- /**
- * Returns null as {@link NomenclaturalCode nomenclatural code} that governs
- * the construction of <i>this</i> non viral taxon name since there is no specific
- * nomenclatural code defined. The real implementention takes place in the
- * subclasses {@link BacterialName BacterialName},
- * {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName} and
- * {@link ZoologicalName ZoologicalName}.
- * This method overrides the {@link TaxonNameBase#getNomenclaturalCode()} method from {@link TaxonNameBase TaxonNameBase}.
- *
- * @return null
- * @see #isCodeCompliant()
- * @see TaxonNameBase#getHasProblem()
- */
- @Override
- @Transient
- public NomenclaturalCode getNomenclaturalCode() {
- logger.warn("Non Viral Name has no specific Code defined. Use subclasses");
- return null;
- }
-
- /**
- * Returns the boolean value of the flag intended to protect (true)
- * or not (false) the {@link #getAuthorshipCache() authorshipCache} (complete authorship string)
- * of <i>this</i> non viral taxon name.
- *
- * @return the boolean value of the protectedAuthorshipCache flag
- * @see #getAuthorshipCache()
- */
- public boolean isProtectedAuthorshipCache() {
- return protectedAuthorshipCache;
- }
-
- /**
- * @see #isProtectedAuthorshipCache()
- * @see #getAuthorshipCache()
- */
- public void setProtectedAuthorshipCache(boolean protectedAuthorshipCache) {
- this.protectedAuthorshipCache = protectedAuthorshipCache;
- }
-
-
- /**
- * Returns the boolean value of the flag indicating whether the name of <i>this</i>
- * botanical taxon name is a hybrid formula (true) or not (false). A hybrid
- * named by a hybrid formula (composed with its parent names by placing the
- * multiplication sign between them) does not have an own published name
- * and therefore has neither an {@link NonViralName#getAuthorshipCache() autorship}
- * nor other name components. If this flag is set no other hybrid flags may
- * be set.
- *
- * @return the boolean value of the isHybridFormula flag
- * @see #isMonomHybrid()
- * @see #isBinomHybrid()
- * @see #isTrinomHybrid()
- */
- public boolean isHybridFormula(){
- return this.hybridFormula;
- }
-
- /**
- * @see #isHybridFormula()
- */
- public void setHybridFormula(boolean hybridFormula){
- this.hybridFormula = hybridFormula;
- }
-
- /**
- * Returns the boolean value of the flag indicating whether <i>this</i> botanical
- * taxon name is the name of an intergeneric hybrid (true) or not (false).
- * In this case the multiplication sign is placed before the scientific
- * name. If this flag is set no other hybrid flags may be set.
- *
- * @return the boolean value of the isMonomHybrid flag
- * @see #isHybridFormula()
- * @see #isBinomHybrid()
- * @see #isTrinomHybrid()
- */
- public boolean isMonomHybrid(){
- return this.monomHybrid;
- }
-
- /**
- * @see #isMonomHybrid()
- * @see #isBinomHybrid()
- * @see #isTrinomHybrid()
- */
- public void setMonomHybrid(boolean monomHybrid){
- this.monomHybrid = monomHybrid;
- }
-
- /**
- * Returns the boolean value of the flag indicating whether <i>this</i> botanical
- * taxon name is the name of an interspecific hybrid (true) or not (false).
- * In this case the multiplication sign is placed before the species
- * epithet. If this flag is set no other hybrid flags may be set.
- *
- * @return the boolean value of the isBinomHybrid flag
- * @see #isHybridFormula()
- * @see #isMonomHybrid()
- * @see #isTrinomHybrid()
- */
- public boolean isBinomHybrid(){
- return this.binomHybrid;
- }
-
- /**
- * @see #isBinomHybrid()
- * @see #isMonomHybrid()
- * @see #isTrinomHybrid()
- */
- public void setBinomHybrid(boolean binomHybrid){
- this.binomHybrid = binomHybrid;
- }
-
- /**
- * Returns the boolean value of the flag indicating whether <i>this</i> botanical
- * taxon name is the name of an infraspecific hybrid (true) or not (false).
- * In this case the term "notho-" (optionally abbreviated "n-") is used as
- * a prefix to the term denoting the infraspecific rank of <i>this</i> botanical
- * taxon name. If this flag is set no other hybrid flags may be set.
- *
- * @return the boolean value of the isTrinomHybrid flag
- * @see #isHybridFormula()
- * @see #isMonomHybrid()
- * @see #isBinomHybrid()
- */
- public boolean isTrinomHybrid(){
- return this.trinomHybrid;
- }
-
- /**
- * @see #isTrinomHybrid()
- * @see #isBinomHybrid()
- * @see #isMonomHybrid()
- */
- public void setTrinomHybrid(boolean trinomHybrid){
- this.trinomHybrid = trinomHybrid;
- }
-
-
- /**
- * Returns the set of all {@link HybridRelationship hybrid relationships}
- * in which <i>this</i> taxon name is involved as a {@link common.RelationshipBase#getRelatedFrom() parent}.
- *
- * @see #getHybridRelationships()
- * @see #getChildRelationships()
- * @see HybridRelationshipType
- */
- public Set<HybridRelationship> getHybridParentRelations() {
- if(hybridParentRelations == null) {
- this.hybridParentRelations = new HashSet<HybridRelationship>();
- }
- return hybridParentRelations;
- }
-
- private void setHybridParentRelations(Set<HybridRelationship> hybridParentRelations) {
- this.hybridParentRelations = hybridParentRelations;
}
-
- /**
- * Returns the set of all {@link HybridRelationship hybrid relationships}
- * in which <i>this</i> taxon name is involved as a {@link common.RelationshipBase#getRelatedTo() child}.
- *
- * @see #getHybridRelationships()
- * @see #getParentRelationships()
- * @see HybridRelationshipType
- */
- public Set<HybridRelationship> getHybridChildRelations() {
- if(hybridChildRelations == null) {
- this.hybridChildRelations = new HashSet<HybridRelationship>();
- }
- return hybridChildRelations;
- }
-
- private void setHybridChildRelations(Set<HybridRelationship> hybridChildRelations) {
- this.hybridChildRelations = hybridChildRelations;
- }
-
- /**
- * Returns the hybrid child relationships ordered by relationship type, or if equal
- * by title cache of the related names.
- * @see #getHybridParentRelations()
- */
- @Transient
- public List<HybridRelationship> getOrderedChildRelationships(){
- List<HybridRelationship> result = new ArrayList<HybridRelationship>();
- result.addAll(this.hybridChildRelations);
- Collections.sort(result);
- Collections.reverse(result);
- return result;
-
+ protected NonViralName(Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorship, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
+ super(rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorship, nomenclaturalReference, nomenclMicroRef, homotypicalGroup);
}
- /**
- * Adds the given {@link HybridRelationship hybrid relationship} to the set
- * of {@link #getHybridRelationships() hybrid relationships} of both non-viral names
- * involved in this hybrid relationship. One of both non-viral names
- * must be <i>this</i> non-viral name otherwise no addition will be carried
- * out. The {@link eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedTo() child
- * non viral taxon name} must be a hybrid, which means that one of its four hybrid flags must be set.
- *
- * @param relationship the hybrid relationship to be added
- * @see #isHybridFormula()
- * @see #isMonomHybrid()
- * @see #isBinomHybrid()
- * @see #isTrinomHybrid()
- * @see #getHybridRelationships()
- * @see #getParentRelationships()
- * @see #getChildRelationships()
- * @see #addRelationship(RelationshipBase)
- * @throws IllegalArgumentException
- */
- protected void addHybridRelationship(HybridRelationship rel) {
- if (rel!=null && rel.getHybridName().equals(this)){
- this.hybridChildRelations.add(rel);
- }else if(rel!=null && rel.getParentName().equals(this)){
- this.hybridParentRelations.add(rel);
- }else{
- throw new IllegalArgumentException("Hybrid relationship is either null or the relationship does not reference this name");
- }
- }
-
-
-
- /**
- * Does the same as the addHybridRelationship method if the given
- * {@link common.RelationshipBase relation} is also a {@link HybridRelationship hybrid relationship}.
- * Otherwise this method does the same as the overwritten {@link TaxonNameBase#addRelationship(RelationshipBase) addRelationship}
- * method from TaxonNameBase.
- *
- * @param relation the relationship to be added to some of <i>this</i> taxon name's relationships sets
- * @see #addHybridRelationship(HybridRelationship)
- * @see TaxonNameBase#addRelationship(RelationshipBase)
- * @see TaxonNameBase#addNameRelationship(NameRelationship)
- * @deprecated to be used by RelationshipBase only
- */
- @Override
- @Deprecated //to be used by RelationshipBase only
- public void addRelationship(RelationshipBase relation) {
- if (relation instanceof HybridRelationship){
- addHybridRelationship((HybridRelationship)relation);
- }else {
- super.addRelationship(relation);
- }
- }
-
- /**
- * Creates a new {@link HybridRelationship#HybridRelationship(BotanicalName, BotanicalName, HybridRelationshipType, String) hybrid relationship}
- * to <i>this</i> botanical name. A HybridRelationship may be of type
- * "is first/second parent" or "is male/female parent". By invoking this
- * method <i>this</i> botanical name becomes a hybrid child of the parent
- * botanical name.
- *
- * @param parentName the botanical name of the parent for this new hybrid 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 #addHybridChild(BotanicalName, HybridRelationshipType,String )
- * @see #getRelationsToThisName()
- * @see #getNameRelations()
- * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
- * @see #addNameRelationship(NameRelationship)
- */
- public HybridRelationship addHybridParent(NonViralName parentName, HybridRelationshipType type, String ruleConsidered){
- return new HybridRelationship(this, parentName, type, ruleConsidered);
- }
-
- /**
- * Creates a new {@link HybridRelationship#HybridRelationship(BotanicalName, BotanicalName, HybridRelationshipType, String) hybrid relationship}
- * to <i>this</i> botanical name. A HybridRelationship may be of type
- * "is first/second parent" or "is male/female parent". By invoking this
- * method <i>this</i> botanical name becomes a parent of the hybrid child
- * botanical name.
- *
- * @param childName the botanical name of the child for this new hybrid 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 #addHybridParent(BotanicalName, HybridRelationshipType,String )
- * @see #getRelationsToThisName()
- * @see #getNameRelations()
- * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
- * @see #addNameRelationship(NameRelationship)
- */
- public HybridRelationship addHybridChild(NonViralName childName, HybridRelationshipType type, String ruleConsidered){
- return new HybridRelationship(childName, this, type, ruleConsidered);
- }
-
-
- /**
- * Removes one {@link HybridRelationship hybrid relationship} from the set of
- * {@link #getHybridRelationships() hybrid relationships} in which <i>this</i> botanical taxon name
- * is involved. The hybrid relationship will also be removed from the set
- * belonging to the second botanical taxon name involved.
- *
- * @param relationship the hybrid relationship which should be deleted from the corresponding sets
- * @see #getHybridRelationships()
- */
- public void removeHybridRelationship(HybridRelationship hybridRelation) {
- if (hybridRelation == null) {
- return;
- }
-
- NonViralName<?> parent = hybridRelation.getParentName();
- NonViralName<?> child = hybridRelation.getHybridName();
- if (this.equals(parent)){
- this.hybridParentRelations.remove(hybridRelation);
- child.hybridChildRelations.remove(hybridRelation);
- hybridRelation.setHybridName(null);
- hybridRelation.setParentName(null);
-
- }
- if (this.equals(child)){
- parent.hybridParentRelations.remove(hybridRelation);
- this.hybridChildRelations.remove(hybridRelation);
- hybridRelation.setHybridName(null);
- hybridRelation.setParentName(null);
-
- }
-
-// if (this.equals(parent) || this.equals(child)){
-// hybridRelation.setHybridName(null);
-// hybridRelation.setParentName(null);
-//
-// if (parent != null) {
-// parent.removeHybridRelationship(hybridRelation);
-// }
-//
-// if (child != null) {
-// child.removeHybridRelationship(hybridRelation);
-// }
-//
-// this.hybridChildRelations.remove(hybridRelation);
-// this.hybridParentRelations.remove(hybridRelation);
-// }
- }
-
-
- public void removeHybridChild(NonViralName child) {
- Set<HybridRelationship> hybridRelationships = new HashSet<HybridRelationship>();
- hybridRelationships.addAll(this.getHybridChildRelations());
- hybridRelationships.addAll(this.getHybridParentRelations());
- for(HybridRelationship hybridRelationship : hybridRelationships) {
- // remove name relationship from this side
- if (hybridRelationship.getParentName().equals(this) && hybridRelationship.getHybridName().equals(child)) {
- this.removeHybridRelationship(hybridRelationship);
- }
- }
- }
-
- public void removeHybridParent(NonViralName parent) {
- Set<HybridRelationship> hybridRelationships = new HashSet<HybridRelationship>();
- hybridRelationships.addAll(this.getHybridChildRelations());
- hybridRelationships.addAll(this.getHybridParentRelations());
- for(HybridRelationship hybridRelationship : hybridRelationships) {
- // remove name relationship from this side
- if (hybridRelationship.getParentName().equals(parent) && hybridRelationship.getHybridName().equals(this)) {
- this.removeHybridRelationship(hybridRelationship);
- }
- }
- }
-
- /**
- * Needs to be implemented by those classes that handle autonyms (e.g. botanical names).
- **/
- @Transient
- public boolean isAutonym(){
- return false;
- }
-
-
-// /**
-// * Returns the boolean value indicating whether <i>this</i> names rank is Rank "unranked"
-// * (uuid = 'a965befb-70a9-4747-a18f-624456c65223') but most likely it is an infrageneric rank
-// * due to existing atomized data for the genus epithet and the infrageneric epithet but missing
-// * specific epithet.
-// * Returns false if <i>this</i> names rank is null.
-// *
-// * @see #isSupraGeneric()
-// * @see #isGenus()
-// * @see #isSpeciesAggregate()
-// * @see #isSpecies()
-// * @see #isInfraSpecific()
-// */
-// @Transient
-// public boolean isInfragenericUnranked() {
-// Rank rank = this.getRank();
-// if (rank == null || ! rank.equals(Rank.UNRANKED())){
-// return false;
-// }
-// if (StringUtils.isBlank(this.getSpecificEpithet()) && StringUtils.isBlank(this.getInfraSpecificEpithet()) ){
-// return true;
-// }else{
-// return false;
-// }
-// }
-
-
- /**
- * Tests if the given name has any authors.
- * @return false if no author ((ex)combination or (ex)basionym) exists, true otherwise
- */
- public boolean hasAuthors() {
- return (this.getCombinationAuthorTeam() != null ||
- this.getExCombinationAuthorTeam() != null ||
- this.getBasionymAuthorTeam() != null ||
- this.getExBasionymAuthorTeam() != null);
- }
-
- /**
- * Shortcut. Returns the combination authors title cache. Returns null if no combination author exists.
- * @return
- */
- public String computeCombinationAuthorNomenclaturalTitle() {
- return computeNomenclaturalTitle(this.getCombinationAuthorTeam());
- }
-
- /**
- * Shortcut. Returns the basionym authors title cache. Returns null if no basionym author exists.
- * @return
- */
- public String computeBasionymAuthorNomenclaturalTitle() {
- return computeNomenclaturalTitle(this.getBasionymAuthorTeam());
- }
-
-
- /**
- * Shortcut. Returns the ex-combination authors title cache. Returns null if no ex-combination author exists.
- * @return
- */
- public String computeExCombinationAuthorNomenclaturalTitle() {
- return computeNomenclaturalTitle(this.getExCombinationAuthorTeam());
- }
-
- /**
- * Shortcut. Returns the ex-basionym authors title cache. Returns null if no exbasionym author exists.
- * @return
- */
- public String computeExBasionymAuthorNomenclaturalTitle() {
- return computeNomenclaturalTitle(this.getExBasionymAuthorTeam());
- }
-
- private String computeNomenclaturalTitle(INomenclaturalAuthor author){
- if (author == null){
- return null;
- }else{
- return author.getNomenclaturalTitle();
- }
- }
-
//*********************** CLONE ********************************************************/
- /**
- * Clones <i>this</i> non-viral name. This is a shortcut that enables to create
- * a new instance that differs only slightly from <i>this</i> non-viral name by
- * modifying only some of the attributes.
- *
- * @see eu.etaxonomy.cdm.model.name.TaxonNameBase#clone()
- * @see java.lang.Object#clone()
- */
@Override
public Object clone() {
NonViralName<?> result = (NonViralName<?>)super.clone();
- //HybridChildRelations
- result.hybridChildRelations = new HashSet<HybridRelationship>();
- for (HybridRelationship hybridRelationship : getHybridChildRelations()){
- HybridRelationship newChildRelationship = (HybridRelationship)hybridRelationship.clone();
- newChildRelationship.setRelatedTo(result);
- result.hybridChildRelations.add(newChildRelationship);
- }
-
- //HybridParentRelations
- result.hybridParentRelations = new HashSet<HybridRelationship>();
- for (HybridRelationship hybridRelationship : getHybridParentRelations()){
- HybridRelationship newParentRelationship = (HybridRelationship)hybridRelationship.clone();
- newParentRelationship.setRelatedFrom(result);
- result.hybridParentRelations.add(newParentRelationship);
- }
-
- //empty caches
- if (! protectedNameCache){
- result.nameCache = null;
- }
-
- //empty caches
- if (! protectedAuthorshipCache){
- result.authorshipCache = null;
- }
-
- //no changes to: basionamyAuthorTeam, combinationAuthorTeam, exBasionymAuthorTeam, exCombinationAuthorTeam
- //genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet,
- //protectedAuthorshipCache, protectedNameCache
- //binomHybrid, monomHybrid, trinomHybrid, hybridFormula,
+ //no changes to:
return result;
}
}
BGBM BDI Projects / cdmlib.git / blobdiff