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.model.agent.TeamOrPersonBase;
import eu.etaxonomy.cdm.model.common.IParsable;
import eu.etaxonomy.cdm.model.common.IRelated;
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
import org.apache.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.Index;
import org.hibernate.annotations.Target;
import eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy;
/**
* The upmost (abstract) class for scientific taxon names regardless of any
- * particular nomenclatural code. The scientific name including author strings and
- * maybe year can be stored as a string in the inherited {@link common.IdentifiableEntity#getTitleCache() titleCache} attribute.
- * The scientific name string without author strings and year can be stored in the {@link #getNameCache() nameCache} attribute.
- * 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})
+ * particular 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}.
*
@Inheritance(strategy=InheritanceType.SINGLE_TABLE)
public abstract class TaxonNameBase<T extends TaxonNameBase, S extends INameCacheStrategy> extends IdentifiableEntity<TaxonNameBase> implements IReferencedEntity, IParsable, IRelated {
static Logger logger = Logger.getLogger(TaxonNameBase.class);
- //Non-atomised addition to a name not ruled by a nomenclatural code
private String appendedPhrase;
private String nomenclaturalMicroReference;
private boolean hasProblem = false;
protected Set<NameTypeDesignation> nameTypeDesignations = new HashSet<NameTypeDesignation>();
+ private Set<SpecimenTypeDesignation> specimenTypeDesignations = new HashSet<SpecimenTypeDesignation>();
private HomotypicalGroup homotypicalGroup = new HomotypicalGroup();
private Set<NameRelationship> relationsFromThisName = new HashSet<NameRelationship>();
private Set<NameRelationship> relationsToThisName = new HashSet<NameRelationship>();
private Rank rank;
private INomenclaturalReference nomenclaturalReference;
- protected boolean protectedNameCache;
-
static Method methodTaxonBaseSetName;
// ************* CONSTRUCTORS *************/
/**
- * Class constructor: creates a new empty taxon name instance.
+ * Class constructor: creates a new empty taxon name.
*
* @see #TaxonNameBase(Rank)
* @see #TaxonNameBase(HomotypicalGroup)
this(null, null);
}
/**
- * Class constructor: creates a new taxon name instance
+ * Class constructor: creates a new taxon name
* only containing its {@link common.Rank rank}.
*
* @param rank the rank to be assigned to this taxon name
this(rank, null);
}
/**
- * Class constructor: creates a new taxon name instance
+ * Class constructor: creates a new taxon name
* only containing its {@link common.HomotypicalGroup homotypical group}.
- * The new taxon name instance will be also added to the set of taxon names
+ * The new taxon name will be also added to the set of taxon names
* belonging to this homotypical group. If the homotypical group
* does not exist a new instance will be created for it.
*
this(null, homotypicalGroup);
}
/**
- * Class constructor: creates a new instance of a taxon name
+ * Class constructor: creates a new taxon name
* only containing its {@link common.Rank rank} and
* its {@link common.HomotypicalGroup homotypical group}.
*
//********* METHODS **************************************/
+ //@Index(name="TaxonNameBaseTitleCacheIndex")
+// public String getTitleCache(){
+// return super.getTitleCache();
+// }
/**
* Returns the boolean value "true" if the components of this taxon name
* follow the rules of the corresponding {@link NomenclaturalCode nomenclatural code},
- * "false" otherwise. The nomenclatural code depends on
+ * "false" otherwise. 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})
}
/**
- * Returns the boolean value of the flag indicating whether the
- * or not (false) the {@link #getNameCache() nameCache} (scientific name without author strings and year)
- * string of this taxon name. This flag shows whether the getNameCache
- * method should return a generated value (false) or the present name cache
- * string (true).
+ * 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 this taxon name.
*
- * @return the boolean value of the protectedNameCache flag
+ * @return the boolean value of the hasProblem flag
* @see #getNameCache()
*/
- //this flag will be set to true if the parseName method was unable to successfully parse the name
public boolean getHasProblem(){
return this.hasProblem;
}
this.hasProblem = hasProblem;
}
/**
+ * Returns exactly the same boolean value as the {@link #getHasProblem() getHasProblem} method.
+ *
* @see #getHasProblem()
*/
public boolean hasProblem(){
}
+ /**
+ * Returns the set of {@link NameTypeDesignation name type designations} assigned
+ * to this 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 addTypeDesignation(TaxonNameBase typeSpecies, ReferenceBase citation, String citationMicroReference, String originalNameString, boolean isRejectedType, boolean isConservedType) {
+ /**
+ * Creates and adds a new {@link NameTypeDesignation name type designation}
+ * to this taxon name's set of name type designations.
+ *
+ * @param typeSpecies the taxon name to be used as type of this 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 used in the reference to assert this designation
+ * @param isRejectedType the boolean status for rejected
+ * @param isConservedType the boolean status for conserved
+ * @see #getNameTypeDesignations()
+ * @see #addTypeDesignation(Specimen, TypeDesignationStatus, ReferenceBase, String, String)
+ */
+ public void addNameTypeDesignation(TaxonNameBase typeSpecies, ReferenceBase citation, String citationMicroReference, String originalNameString, boolean isRejectedType, boolean isConservedType) {
NameTypeDesignation td = new NameTypeDesignation(this, typeSpecies, citation, citationMicroReference, originalNameString, isRejectedType, isConservedType);
}
- public void addTypeDesignation(Specimen typeSpecimen, TypeDesignationStatus status, ReferenceBase citation, String citationMicroReference, String originalNameString) {
- this.homotypicalGroup.addTypeDesignation(typeSpecimen, status, citation, citationMicroReference, originalNameString);
- }
- public void removeTypeDesignation(NameTypeDesignation typeDesignation) {
+
+ /**
+ * Removes one element from the set of {@link NameTypeDesignation name type designations} of this taxon name.
+ * The name type designation itself will be nullified.
+ *
+ * @param typeDesignation the name type designation of this 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);
}
+
+ /**
+ * @return the specimenTypeDesignations
+ */
+ @ManyToMany
+ @Cascade(CascadeType.SAVE_UPDATE)
+ public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations() {
+ return specimenTypeDesignations;
+ }
+ /**
+ * @param specimenTypeDesignations the specimenTypeDesignations to set
+ */
+ protected void setSpecimenTypeDesignations(Set<SpecimenTypeDesignation> specimenTypeDesignations) {
+ this.specimenTypeDesignations = specimenTypeDesignations;
+ }
+
+ /**
+ * Returns the set of {@link SpecimenTypeDesignation specimen type designations} assigned
+ * indirectly to this taxon name through its {@link HomotypicalGroup homotypical group}.
+ * The rank of this 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}
+ * to the set of specimen type designations assigned to the
+ * {@link HomotypicalGroup homotypical group} to which this taxon name belongs.
+ *
+ * @param typeSpecimen the specimen to be used as a type for this 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
+ protected void addSpecimenTypeDesignation(SpecimenTypeDesignation specimenTypeDesignation) {
+ this.specimenTypeDesignations.add(specimenTypeDesignation);
+ }
+
+ //only to be used for xxx
+ 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 this 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 #removeTypeDesignation(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
+ * this 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() {
@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 this taxon name.
+ *
+ * @see reference.INomenclaturalReference#getNomenclaturalCitation()
+ * @see #getNomenclaturalReference()
+ * @see #getNomenclaturalMicroReference()
+ */
@Transient
public String getCitationString(){
logger.warn("getCitationString not yet implemented");
}
/**
- * returns year of according nomenclatural reference, null if nomenclatural
- * reference does not exist
+ * Returns the string containing the publication date (generally only year)
+ * of the nomenclatural reference, null if there is no nomenclatural
+ * reference.
+ *
+ * @see reference.INomenclaturalReference#getYear()
*/
@Transient
public String getReferenceYear(){
}
}
+ /**
+ * Returns the set of {@link taxon.TaxonBase taxon bases} that refer to this 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.EAGER)
public Set<TaxonBase> getTaxonBases() {
return this.taxonBases;
}
+ /**
+ * @see #getTaxonBases()
+ */
protected void setTaxonBases(Set<TaxonBase> taxonBases) {
if (taxonBases == null){
taxonBases = new HashSet<TaxonBase>();
this.taxonBases = taxonBases;
}
}
+ /**
+ * Adds a new {@link taxon.TaxonBase taxon base}
+ * to the set of taxon bases using this taxon name.
+ *
+ * @param taxonBase the taxon base to be added
+ * @see #getTaxonBases()
+ */
//TODO protected
public void addTaxonBase(TaxonBase taxonBase){
taxonBases.add(taxonBase);
initMethods();
invokeSetMethod(methodTaxonBaseSetName, taxonBase);
}
+ public void removeTaxonBase(TaxonBase taxonBase){
+ taxonBases.remove(taxonBase);
+ initMethods();
+ invokeSetMethodWithNull(methodTaxonBaseSetName, taxonBase);
+ }
private void initMethods(){
if (methodTaxonBaseSetName == null){
/**
- * Return a set of taxa that use this name.
- * @return Set<Taxon> The set of taxa this TaxonName belongs to
+ * Returns the set of {@link taxon.Taxon taxa} ("accepted/correct" names according to any
+ * reference) that are based on this 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(){
}
/**
- * Return a set of synonyms that use this name
- * @return The set of synonyms this TaxonName belongs to
+ * Returns the set of {@link taxon.Synonym (junior) synonyms} (according to any
+ * reference) that are based on this 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() {
return result;
}
- @Transient
- public Set<SpecimenTypeDesignation> getSpecimenTypeDesignations() {
- return this.getHomotypicalGroup().getTypeDesignations();
- }
-
// ***********
+ /**
+ * Returns the boolean value indicating whether a given taxon name belongs
+ * to the same {@link HomotypicalGroup homotypical group} as this 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;
//********* Rank comparison shortcuts ********************//
+ /**
+ * Returns the boolean value indicating whether the taxonomic rank of this
+ * taxon name is higher than the genus rank (true) or not (false).
+ * Suprageneric non viral names are monomials.
+ *
+ * @see #isGenus()
+ * @see #isInfraGeneric()
+ * @see #isSpecies()
+ * @see #isInfraSpecific()
+ */
@Transient
public boolean isSupraGeneric() {
return getRank().isSupraGeneric();
}
+ /**
+ * Returns the boolean value indicating whether the taxonomic rank of this
+ * taxon name is the genus rank (true) or not (false). Non viral names with
+ * genus rank are monomials.
+ *
+ * @see #isSupraGeneric()
+ * @see #isInfraGeneric()
+ * @see #isSpecies()
+ * @see #isInfraSpecific()
+ */
@Transient
public boolean isGenus() {
return getRank().isGenus();
}
+ /**
+ * Returns the boolean value indicating whether the taxonomic rank of this
+ * taxon name is higher than the species rank and lower than
+ * the genus rank (true) or not (false). Infrageneric non viral names
+ * are binomials.
+ *
+ * @see #isSupraGeneric()
+ * @see #isGenus()
+ * @see #isSpecies()
+ * @see #isInfraSpecific()
+ */
@Transient
public boolean isInfraGeneric() {
return getRank().isInfraGeneric();
}
+ /**
+ * Returns the boolean value indicating whether the taxonomic rank of this
+ * taxon name is the species rank (true) or not (false). Non viral names
+ * with species rank are binomials.
+
+ *
+ * @see #isSupraGeneric()
+ * @see #isGenus()
+ * @see #isInfraGeneric()
+ * @see #isInfraSpecific()
+ */
@Transient
public boolean isSpecies() {
return getRank().isSpecies();
}
+ /**
+ * Returns the boolean value indicating whether the taxonomic rank of this
+ * taxon name is lower than the species rank (true) or not (false).
+ * Infraspecific non viral names are trinomials.
+ *
+ * @see #isSupraGeneric()
+ * @see #isGenus()
+ * @see #isInfraGeneric()
+ * @see #isSpecies()
+ */
@Transient
public boolean isInfraSpecific() {
return getRank().isInfraSpecific();
}
+ /**
+ * Returns the {@link NomenclaturalCode nomenclatural code} that governs
+ * the construction of this taxon name. Each taxon name is governed by one
+ * and only one nomenclatural code.
+ *
+ * @see #isCodeCompliant()
+ * @see #getHasProblem()
+ */
@Transient
abstract public NomenclaturalCode getNomeclaturalCode();
- @Override
- public String generateTitle() {
- // TODO Auto-generated method stub
- return null;
- }
}
\ No newline at end of file
BGBM BDI Projects / cdmlib.git / blobdiff