package eu.etaxonomy.cdm.model.name;
-import java.util.HashSet;
-import java.util.Set;
+import java.util.Map;
import javax.persistence.Entity;
-import javax.persistence.OneToMany;
-import javax.persistence.Transient;
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.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
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.Indexed;
+import org.springframework.beans.factory.annotation.Configurable;
+import eu.etaxonomy.cdm.common.CdmUtils;
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
-import eu.etaxonomy.cdm.model.common.RelationshipBase;
+import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
import eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy;
import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "BotanicalName", propOrder = {
- "isHybridFormula",
- "isMonomHybrid",
- "isBinomHybrid",
- "isTrinomHybrid",
- "isAnamorphic",
- "hybridRelationships"
+ "anamorphic"
})
@XmlRootElement(name = "BotanicalName")
@Entity
-public class BotanicalName extends NonViralName {
-
+@Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")
+@Audited
+@Configurable
+public class BotanicalName extends NonViralName<BotanicalName> implements Cloneable /*, IMergable*/ {
+ private static final long serialVersionUID = 6818651572463497727L;
+ @SuppressWarnings("unused")
private static final Logger logger = Logger.getLogger(BotanicalName.class);
- //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")
- private boolean isHybridFormula = false;
-
- @XmlElement(name ="IsMonomHybrid")
- private boolean isMonomHybrid = false;
-
- @XmlElement(name ="IsBinomHybrid")
- private boolean isBinomHybrid = false;
-
- @XmlElement(name ="IsTrinomHybrid")
- private boolean isTrinomHybrid = false;
-
//Only for fungi: to indicate that the type of the name is asexual or not
@XmlElement(name ="IsAnamorphic")
- private boolean isAnamorphic;
-
- @XmlElementWrapper(name = "HybridRelationships")
- @XmlElement(name = "HybridRelationship")
- private Set<HybridRelationship> hybridRelationships = new HashSet();
+ private boolean anamorphic;
- static private INonViralNameParser nameParser = new NonViralNameParserImpl();
+ static private INonViralNameParser<?> nameParser = new NonViralNameParserImpl();
// ************* CONSTRUCTORS *************/
//needed by hibernate
if (nameParser == null){
nameParser = new NonViralNameParserImpl();
}
- return (BotanicalName)nameParser.parseFullName(fullNameString, NomenclaturalCode.ICBN(), rank);
+ return (BotanicalName)nameParser.parseFullName(fullNameString, NomenclaturalCode.ICNAFP, rank);
}
/**
if (nameParser == null){
nameParser = new NonViralNameParserImpl();
}
- return (BotanicalName)nameParser.parseReferencedName(fullNameAndReferenceString, NomenclaturalCode.ICBN(), rank);
- }
-
-
- /**
- * Returns the set of all {@link HybridRelationship hybrid relationships}
- * in which <i>this</i> botanical taxon name is involved. Any botanical taxon name
- * (even itself a hybrid taxon name) can be a parent of another hybrid
- * taxon name.
- *
- * @see #getParentRelationships()
- * @see #getChildRelationships()
- * @see #addHybridRelationship(HybridRelationship)
- * @see #addRelationship(RelationshipBase)
- */
- @OneToMany
- @Cascade({CascadeType.SAVE_UPDATE, CascadeType.DELETE_ORPHAN})
- public Set<HybridRelationship> getHybridRelationships() {
- return hybridRelationships;
- }
- /**
- * @see #getHybridRelationships()
- */
- protected void setHybridRelationships(Set<HybridRelationship> relationships) {
- this.hybridRelationships = relationships;
- }
- /**
- * Adds the given {@link HybridRelationship hybrid relationship} to the set
- * of {@link #getHybridRelationships() hybrid relationships} of both botanical taxon names
- * involved in this hybrid relationship. One of both botanical taxon names
- * must be <i>this</i> botanical taxon name otherwise no addition will be carried
- * out. The {@link eu.etaxonomy.cdm.model.common.RelationshipBase#getRelatedTo() child botanical 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)
- */
- protected void addHybridRelationship(HybridRelationship relationship) {
- this.hybridRelationships.add(relationship);
- }
-
- /**
- * 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
- * @see #addHybridChild(BotanicalName, HybridRelationshipType,String )
- * @see #getRelationsToThisName()
- * @see #getNameRelations()
- * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
- * @see #addNameRelationship(NameRelationship)
- */
- public void addHybridParent(BotanicalName parentName, HybridRelationshipType type, String ruleConsidered){
- HybridRelationship rel = 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
- * @see #addHybridParent(BotanicalName, HybridRelationshipType,String )
- * @see #getRelationsToThisName()
- * @see #getNameRelations()
- * @see #addRelationshipFromName(TaxonNameBase, NameRelationshipType, String)
- * @see #addNameRelationship(NameRelationship)
- */
- public void addHybridChild(BotanicalName childName, HybridRelationshipType type, String ruleConsidered){
- HybridRelationship rel = 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 relationship) {
- //TODO
- logger.warn("Birelationship not yet implemented");
- this.hybridRelationships.remove(relationship);
+ return (BotanicalName)nameParser.parseReferencedName(fullNameAndReferenceString, NomenclaturalCode.ICNAFP, rank);
}
- /**
- * Returns the set of all {@link HybridRelationship hybrid relationships}
- * in which <i>this</i> botanical taxon name is involved as a {@link common.RelationshipBase#getRelatedFrom() parent}.
- *
- * @see #getHybridRelationships()
- * @see #getChildRelationships()
- * @see HybridRelationshipType
- */
- @Transient
- public Set<HybridRelationship> getParentRelationships() {
- // FIXME: filter relations
- return hybridRelationships;
- }
- /**
- * Returns the set of all {@link HybridRelationship hybrid relationships}
- * in which <i>this</i> botanical taxon name is involved as a {@link common.RelationshipBase#getRelatedTo() child}.
- *
- * @see #getHybridRelationships()
- * @see #getParentRelationships()
- * @see HybridRelationshipType
- */
- @Transient
- public Set<HybridRelationship> getChildRelationships() {
- // FIXME: filter relations
- return hybridRelationships;
- }
+//***********************
- /**
- * 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)
- */
+ private static Map<String, java.lang.reflect.Field> allFields = null;
@Override
- @Deprecated //To be used by RelationshipBase only
- public void addRelationship(RelationshipBase relation) {
- if (relation instanceof HybridRelationship){
- addHybridRelationship((HybridRelationship)relation);
- }else {
- super.addRelationship(relation);
+ protected Map<String, java.lang.reflect.Field> getAllFields(){
+ if (allFields == null){
+ allFields = CdmUtils.getAllFields(this.getClass(), CdmBase.class, false, false, false, true);
}
- }
-
- /**
- * 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.isHybridFormula;
- }
-
- /**
- * @see #isHybridFormula()
- */
- public void setHybridFormula(boolean isHybridFormula){
- this.isHybridFormula = isHybridFormula;
- }
-
- /**
- * 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.isMonomHybrid;
- }
-
- /**
- * @see #isMonomHybrid()
- * @see #isBinomHybrid()
- * @see #isTrinomHybrid()
- */
- public void setMonomHybrid(boolean isMonomHybrid){
- this.isMonomHybrid = isMonomHybrid;
- }
-
- /**
- * 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.isBinomHybrid;
- }
-
- /**
- * @see #isBinomHybrid()
- * @see #isMonomHybrid()
- * @see #isTrinomHybrid()
- */
- public void setBinomHybrid(boolean isBinomHybrid){
- this.isBinomHybrid = isBinomHybrid;
- }
-
- /**
- * 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.isTrinomHybrid;
- }
-
- /**
- * @see #isTrinomHybrid()
- * @see #isBinomHybrid()
- * @see #isMonomHybrid()
- */
- public void setTrinomHybrid(boolean isTrinomHybrid){
- this.isTrinomHybrid = isTrinomHybrid;
- }
+ return allFields;
+ }
+//*************************
+
/**
* Returns the boolean value of the flag indicating whether the specimen
* type of <i>this</i> botanical taxon name for a fungus is asexual (true) or not
* @return the boolean value of the isAnamorphic flag
*/
public boolean isAnamorphic(){
- return this.isAnamorphic;
+ return this.anamorphic;
}
/**
* @see #isAnamorphic()
*/
- public void setAnamorphic(boolean isAnamorphic){
- this.isAnamorphic = isAnamorphic;
+ public void setAnamorphic(boolean anamorphic){
+ this.anamorphic = anamorphic;
}
* @see NonViralName#isCodeCompliant()
* @see TaxonNameBase#getHasProblem()
*/
- @Transient
@Override
public NomenclaturalCode getNomenclaturalCode(){
- return NomenclaturalCode.ICBN();
+ return NomenclaturalCode.ICNAFP;
+ }
+
+ /**
+ * Checks if this name is an autonym.<BR>
+ * An autonym is a taxon name that has equal specific and infra specific epithets.<BR>
+ * {@link http://ibot.sav.sk/icbn/frameset/0010Ch2Sec1a006.htm#6.8. Vienna Code ยง6.8}
+ * @return true, if name has Rank, Rank is below species and species epithet equals infraSpeciesEpithtet, else false
+ */
+ @Override
+ public boolean isAutonym(){
+ if (this.getRank() != null && this.getSpecificEpithet() != null && this.getInfraSpecificEpithet() != null &&
+ this.getRank().isInfraSpecific() && this.getSpecificEpithet().trim().equals(this.getInfraSpecificEpithet().trim())){
+ return true;
+ }else{
+ return false;
+ }
+ }
+
+//*********************** CLONE ********************************************************/
+
+ /**
+ * Clones <i>this</i> botanical name. This is a shortcut that enables to create
+ * a new instance that differs only slightly from <i>this</i> botanical name by
+ * modifying only some of the attributes.
+ *
+ * @see eu.etaxonomy.cdm.model.name.NonViralName#clone()
+ * @see java.lang.Object#clone()
+ */
+ @Override
+ public Object clone() {
+ BotanicalName result = (BotanicalName)super.clone();
+ //no changes to: title, authorTeam, hasProblem, nomenclaturallyRelevant, uri
+ return result;
}
+
}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff