public class NonViralName<T extends NonViralName> extends TaxonNameBase<NonViralName, INonViralNameCacheStrategy> {
private static final Logger logger = Logger.getLogger(NonViralName.class);
- //The scientific name without author strings and year
private String nameCache;
- //The suprageneric or the genus name
private String genusOrUninomial;
- //Genus subdivision epithet
private String infraGenericEpithet;
- //species epithet
private String specificEpithet;
- //Species subdivision epithet
private String infraSpecificEpithet;
- //Author team that published the present combination
private INomenclaturalAuthor combinationAuthorTeam;
- //Author team that contributed to the publication of the present combination
private INomenclaturalAuthor exCombinationAuthorTeam;
- //Author team that published the original combination
private INomenclaturalAuthor basionymAuthorTeam;
- //Author team that contributed to the original publication of the name
private INomenclaturalAuthor exBasionymAuthorTeam;
- //concatenated und formated author teams including basionym and combination authors
private String authorshipCache;
- //this flag shows if the getAuthorshipCache should return generated value(false) or the given String(true)
protected boolean protectedAuthorshipCache;
protected boolean protectedNameCache;
//needed by hibernate
/**
* Class constructor: creates a new non viral taxon name instance
- * only containing the {@link eu.etaxonomy.cdm.strategy.cache.NonViralNameDefaultCacheStrategy default cache strategy}
- * for building its scientific taxon name string without authors nor year.
+ * only containing the {@link eu.etaxonomy.cdm.strategy.cache.NonViralNameDefaultCacheStrategy default cache strategy}.
*
* @see #NonViralName(Rank, HomotypicalGroup)
* @see #NonViralName(Rank, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
+ * @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.IIdentifiableEntityCacheStrategy
*/
protected NonViralName(){
super();
* Class constructor: creates a new non viral taxon name instance
* only containing its {@link common.Rank rank},
* its {@link common.HomotypicalGroup homotypical group} and
- * only containing the {@link eu.etaxonomy.cdm.strategy.cache.NonViralNameDefaultCacheStrategy default cache strategy}
- * for building its scientific taxon name string without authors nor year.
+ * only containing the {@link eu.etaxonomy.cdm.strategy.cache.NonViralNameDefaultCacheStrategy default cache strategy}.
*
- * @param rank the rank to be assigned to this taxon name
- * @param homotypicalGroup the homotypical group to which this taxon name belongs
+ * @param rank the rank to be assigned to this non viral taxon name
+ * @param homotypicalGroup the homotypical group to which this non viral taxon name belongs
* @see #NonViralName()
* @see #NonViralName(Rank, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
* @see #NewInstance(Rank, HomotypicalGroup)
+ * @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.IIdentifiableEntityCacheStrategy
*/
protected NonViralName(Rank rank, HomotypicalGroup homotypicalGroup) {
super(rank, homotypicalGroup);
* its {@link common.HomotypicalGroup homotypical group},
* its scientific name components, its {@link agent.TeamOrPersonBase author(team)},
* its {@link reference.INomenclaturalReference nomenclatural reference} and
- * the {@link eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy default cache strategy}
- * for building its scientific taxon name string without authors nor year.
+ * the {@link eu.etaxonomy.cdm.strategy.cache.NonViralNameDefaultCacheStrategy default cache strategy}.
*
- * @param rank the rank to be assigned to this taxon name
+ * @param rank the rank to be assigned to this non viral taxon name
* @param genusOrUninomial the string for this taxon name
- * if its rank is genus or above or for the genus component
+ * if its rank is genus or higher or for the genus part
* if its rank is lower than genus
* @param specificEpithet the string for the first epithet of
- * this taxon name if its rank is lower than genus
+ * this non viral taxon name if its rank is lower than genus
* @param infraSpecificEpithet the string for the second epithet of
- * this taxon name if its rank is lower than species
- * @param combinationAuthorTeam the author or the team who published this taxon name
- * @param nomenclaturalReference the nomenclatural reference where this taxon name was published
+ * this non viral taxon name if its rank is lower than species
+ * @param combinationAuthorTeam the author or the team who published this non viral taxon name
+ * @param nomenclaturalReference the nomenclatural reference where this 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 this taxon name belongs
+ * @param homotypicalGroup the homotypical group to which this non viral taxon name belongs
* @see #NonViralName()
* @see #NonViralName(Rank, HomotypicalGroup)
* @see #NewInstance(Rank, HomotypicalGroup)
+ * @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.IIdentifiableEntityCacheStrategy
*/
protected NonViralName(Rank rank, String genusOrUninomial, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorTeam, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
super(rank, homotypicalGroup);
//********* METHODS **************************************/
/**
* Creates a new non viral taxon name instance
- * only containing its {@link common.Rank rank}.
+ * only containing its {@link common.Rank rank} and
+ * the {@link eu.etaxonomy.cdm.strategy.cache.NonViralNameDefaultCacheStrategy default cache strategy}.
*
* @param rank the rank to be assigned to this non viral taxon name
* @see #NewInstance(Rank, HomotypicalGroup)
* @see #NonViralName(Rank, HomotypicalGroup)
* @see #NonViralName()
* @see #NonViralName(Rank, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
+ * @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.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} and
- * its {@link common.HomotypicalGroup homotypical group}.
+ * its {@link common.HomotypicalGroup homotypical group} and
+ * the {@link eu.etaxonomy.cdm.strategy.cache.NonViralNameDefaultCacheStrategy default cache strategy}.
* The new non viral taxon name instance will be also added to the set of
- * taxon names belonging to this homotypical group. If the homotypical
+ * non viral taxon names belonging to this homotypical group. If the homotypical
* group does not exist a new instance will be created for it.
*
* @param rank the rank to be assigned to this non viral taxon name
* @see #NonViralName(Rank, HomotypicalGroup)
* @see #NonViralName()
* @see #NonViralName(Rank, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
+ * @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.IIdentifiableEntityCacheStrategy
*/
public static NonViralName NewInstance(Rank rank, HomotypicalGroup homotypicalGroup){
return new NonViralName(rank, homotypicalGroup);
//TODO for PROTOTYPE
/**
- * Returns the {@link eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy cache strategy} used to generate a name string
- * corresponding to this taxon name. The cache strategy includes
- * two methods: {@link eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy#getNameCache(TaxonNameBase) one} for the scientific name
- * string without author teams and year and another {@link eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy#getTaggedName(TaxonNameBase) another one} for the array of scientific name components
- * with author teams and eventually year.
+ * Returns the {@link eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy cache strategy} used to generate
+ * several strings corresponding to this non viral taxon name
+ * (in particular taxon name caches and author strings).
*
- * @return the name cache strategy used for this taxon name
+ * @return the cache strategy used for this non viral taxon name
+ * @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy
* @see eu.etaxonomy.cdm.strategy.cache.INameCacheStrategy
- * @see eu.etaxonomy.cdm.strategy.cache.NameCacheStrategyBase
+ * @see eu.etaxonomy.cdm.strategy.cache.IIdentifiableEntityCacheStrategy
*/
@Transient
@Override
+ /**
+ * Returns the {@link agent.INomenclaturalAuthor author (team)} that published this non viral
+ * taxon name.
+ *
+ * @return the nomenclatural author (team) of this non viral taxon name
+ * @see agent.INomenclaturalAuthor
+ * @see agent.TeamOrPersonBase#getNomenclaturalTitle()
+ */
@ManyToOne
@Cascade({CascadeType.SAVE_UPDATE})
@Target(TeamOrPersonBase.class)
public INomenclaturalAuthor getCombinationAuthorTeam(){
return this.combinationAuthorTeam;
}
+ /**
+ * @see #getCombinationAuthorTeam()
+ */
public void setCombinationAuthorTeam(INomenclaturalAuthor combinationAuthorTeam){
this.combinationAuthorTeam = combinationAuthorTeam;
}
+ /**
+ * Returns the {@link agent.INomenclaturalAuthor author (team)} that contributed to
+ * the publication of this non viral taxon name as generally stated by
+ * the {@link #getCombinationAuthorTeam() combination author (team)} itself.
+ * The presence of an author (team) of this non viral taxon name is a
+ * condition for the existence of an ex author (team) for this same name.
+ *
+ * @return the nomenclatural ex author (team) of this non viral taxon name
+ * @see #getCombinationAuthorTeam()
+ * @see agent.INomenclaturalAuthor
+ * @see agent.TeamOrPersonBase#getNomenclaturalTitle()
+ */
@ManyToOne
@Cascade({CascadeType.SAVE_UPDATE})
@Target(TeamOrPersonBase.class)
public INomenclaturalAuthor getExCombinationAuthorTeam(){
return this.exCombinationAuthorTeam;
}
+ /**
+ * @see #getExCombinationAuthorTeam()
+ */
public void setExCombinationAuthorTeam(INomenclaturalAuthor exCombinationAuthorTeam){
this.exCombinationAuthorTeam = exCombinationAuthorTeam;
}
+ /**
+ * Returns the {@link agent.INomenclaturalAuthor author (team)} that published the original combination
+ * on which this non viral taxon name is nomenclaturally based. Such an
+ * author (team) can only exist if this non viral taxon name is a new
+ * combination due to a taxonomical revision.
+ *
+ * @return the nomenclatural basionym author (team) of this non viral taxon name
+ * @see #getCombinationAuthorTeam()
+ * @see agent.INomenclaturalAuthor
+ * @see agent.TeamOrPersonBase#getNomenclaturalTitle()
+ */
@ManyToOne
@Cascade({CascadeType.SAVE_UPDATE})
@Target(TeamOrPersonBase.class)
public INomenclaturalAuthor getBasionymAuthorTeam(){
return basionymAuthorTeam;
}
+ /**
+ * @see #getBasionymAuthorTeam()
+ */
public void setBasionymAuthorTeam(INomenclaturalAuthor basionymAuthorTeam) {
this.basionymAuthorTeam = basionymAuthorTeam;
}
+ /**
+ * Returns the {@link agent.INomenclaturalAuthor author (team)} that contributed to
+ * the publication of the original combination this non viral taxon name is
+ * based on. This should have been generally stated by
+ * the {@link #getCombinationAuthorTeam() basionym author (team)} itself.
+ * The presence of a basionym author (team) of this non viral taxon name is a
+ * condition for the existence of an ex basionym author (team)
+ * for this same name.
+ *
+ * @return the nomenclatural ex basionym author (team) of this non viral taxon name
+ * @see #getBasionymAuthorTeam()
+ * @see #getCombinationAuthorTeam()
+ * @see agent.INomenclaturalAuthor
+ * @see agent.TeamOrPersonBase#getNomenclaturalTitle()
+ */
@ManyToOne
@Cascade({CascadeType.SAVE_UPDATE})
@Target(TeamOrPersonBase.class)
public INomenclaturalAuthor getExBasionymAuthorTeam(){
return exBasionymAuthorTeam;
}
+ /**
+ * @see #getExBasionymAuthorTeam()
+ */
public void setExBasionymAuthorTeam(INomenclaturalAuthor exBasionymAuthorTeam) {
this.exBasionymAuthorTeam = exBasionymAuthorTeam;
}
-
+ /**
+ * Returns either the scientific name string (without authorship) for this
+ * 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 this non viral taxon name
+ * @see #getNameCache()
+ */
public String getGenusOrUninomial() {
return genusOrUninomial;
}
+ /**
+ * @see #getGenusOrUninomial()
+ */
public void setGenusOrUninomial(String genusOrUninomial) {
this.genusOrUninomial = genusOrUninomial;
}
+ /**
+ * Returns the genus subdivision epithet string (infrageneric part) for
+ * this non viral taxon name if its {@link Rank rank} is infrageneric (lower than genus and
+ * higher than species aggregate). Genus subdivision epithet strings begin
+ * with an upper case letter.
+ *
+ * @return the string containing the infrageneric part of this non viral taxon name
+ * @see #getNameCache()
+ */
public String getInfraGenericEpithet(){
return this.infraGenericEpithet;
}
/**
- *
- * @param infraGenericEpithet infraGenericEpithet
+ * @see #getInfraGenericEpithet()
*/
public void setInfraGenericEpithet(String infraGenericEpithet){
this.infraGenericEpithet = infraGenericEpithet;
}
+ /**
+ * Returns the species epithet string for this non viral taxon name if its {@link Rank rank} is
+ * species aggregate or lower. Species epithet strings begin with a
+ * lower case letter.
+ *
+ * @return the string containing the species epithet of this non viral taxon name
+ * @see #getNameCache()
+ */
public String getSpecificEpithet(){
return this.specificEpithet;
}
/**
- *
- * @param specificEpithet specificEpithet
+ * @see #getSpecificEpithet()
*/
public void setSpecificEpithet(String specificEpithet){
this.specificEpithet = specificEpithet;
}
+ /**
+ * Returns the species subdivision epithet string (infraspecific part) for
+ * this non viral taxon name if its {@link Rank rank} is infraspecific (lower than species).
+ * Species subdivision epithet strings begin with a lower case letter.
+ *
+ * @return the string containing the infraspecific part of this non viral taxon name
+ * @see #getNameCache()
+ */
public String getInfraSpecificEpithet(){
return this.infraSpecificEpithet;
}
/**
- *
- * @param infraSpecificEpithet infraSpecificEpithet
+ * @see #getInfraSpecificEpithet()
*/
public void setInfraSpecificEpithet(String infraSpecificEpithet){
this.infraSpecificEpithet = infraSpecificEpithet;
}
+ /**
+ * Generates and returns the string with the scientific name of this
+ * non viral taxon name including author strings and maybe year according to
+ * the strategy defined in
+ * {@link eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy INonViralNameCacheStrategy}.
+ * This string may be stored in the inherited
+ * {@link common.IdentifiableEntity#getTitleCache() titleCache} attribute.
+ * This method overrides the generic and inherited
+ * TaxonNameBase#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()
+ * @see TaxonNameBase#generateTitle()
+ */
@Override
public String generateTitle(){
if (cacheStrategy == null){
}
/**
- * Generates the composed name string of this taxon name without author
+ * Generates the composed name string of this non viral taxon name without author
* strings or year according to the strategy defined in
* {@link eu.etaxonomy.cdm.strategy.cache.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 this taxon name without authors or year
+ * @return the string with the composed name of this non viral taxon name without authors or year
+ * @see #getNameCache()
*/
protected String generateNameCache(){
if (cacheStrategy == null){
/**
* Returns or generates the nameCache (scientific name
- * without author strings and year) string for this taxon name. If the
+ * without author strings and year) string for this 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 this taxon name (without authors or year)
+ * @return the string which identifies this non viral taxon name (without authors or year)
* @see #generateNameCache()
*/
public String getNameCache() {
}
/**
- * Assigns a nameCache string to this taxon name and protects it from being overwritten.
+ * Assigns a nameCache string to this non viral taxon name and protects it from being overwritten.
*
- * @param nameCache the string which identifies this taxon name (without authors or year)
+ * @param nameCache the string which identifies this non viral taxon name (without authors or year)
* @see #getNameCache()
*/
public void setNameCache(String nameCache){
/**
* 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 this taxon name.
+ * string of this non viral taxon name.
*
* @return the boolean value of the protectedNameCache flag
* @see #getNameCache()
}
+ /**
+ * Generates and returns a concatenated and formated authorteams string
+ * including basionym and combination authors of this non viral taxon name
+ * according to the strategy defined in
+ * {@link eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy#getAuthorshipCache(NonViralName) INonViralNameCacheStrategy}.
+ *
+ * @return the string with the concatenated and formated authorteams for this non viral taxon name
+ * @see eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy#getAuthorshipCache(NonViralName)
+ */
public String generateAuthorship(){
if (cacheStrategy == null){
logger.warn("No CacheStrategy defined for nonViralName: " + this.getUuid());
}
/**
- * returns concatenated und formated authorteams including basionym and
- * combination authors
+ * Returns the concatenated and formated authorteams string including
+ * basionym and combination authors of this 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 this non viral taxon name
+ * @see #generateAuthorship()
*/
public String getAuthorshipCache() {
if (protectedAuthorshipCache){
return authorshipCache;
}
+ /**
+ * Assigns an authorshipCache string to this non viral taxon name.
+ *
+ * @param authorshipCache the string which identifies the complete authorship of this non viral taxon name
+ * @see #getAuthorshipCache()
+ */
public void setAuthorshipCache(String authorshipCache) {
this.authorshipCache = authorshipCache;
}
+
+
/**
- * Returns the boolean value "true" if the components of this taxon name
+ * Returns the boolean value "true" if the components of this non viral taxon name
* follow the rules of the corresponding {@link NomenclaturalCode nomenclatural code},
- * "false" otherwise. The nomenclature code depends on
+ * "false" otherwise. The nomenclatural code depends on
* the concrete name subclass ({@link BacterialName BacterialName},
- * {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName} ot
- * {@link ZoologicalName ZoologicalName} to which this taxon name belongs.
+ * {@link BotanicalName BotanicalName}, {@link CultivarPlantName CultivarPlantName} or
+ * {@link ZoologicalName ZoologicalName} to which this non viral taxon name belongs.
+ * This method overrides the isCodeCompliant method from {@link TaxonNameBase#isCodeCompliant() TaxonNameBase}.
*
- * @return the boolean value expressing the compliance of this taxon name to the nomenclatural code
+ * @return the boolean value expressing the compliance of this non viral taxon name to its nomenclatural code
+ * @see TaxonNameBase#isCodeCompliant()
*/
@Override
@Transient
/* (non-Javadoc)
* @see eu.etaxonomy.cdm.model.name.TaxonNameBase#getNomeclaturalCode()
*/
+ /**
+ * Returns null as {@link NomenclaturalCode nomenclatural code} that governs
+ * the construction of this 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 getNomeclaturalCode method from {@link TaxonNameBase#getNomeclaturalCode() TaxonNameBase}.
+ *
+ * @return null
+ * @see #isCodeCompliant()
+ * @see TaxonNameBase#getHasProblem()
+ */
@Transient
@Override
public NomenclaturalCode getNomeclaturalCode() {
+ //TODO What is the purpose of overriding the inherited method?
logger.warn("Non Viral Name has no specific Code defined. Use subclasses");
return null;
}
/**
- * Returns the string with the scientific name of this taxon name including
- * author strings and maybe year. This string may be stored in the
- * inherited {@link common.IdentifiableEntity#getTitleCache() titleCache} attribute.
- * This method overrides the generic and inherited
- * IdentifiableEntity#getTitleCache() method.
- *
- * @see common.IdentifiableEntity#getTitleCache()
+ * Returns the boolean value of the flag intended to protect (true)
+ * or not (false) the {@link #getAuthorshipCache() authorshipCache} (complete authorship string)
+ * of this non viral taxon name.
+ *
+ * @return the boolean value of the protectedAuthorshipCache flag
+ * @see #getAuthorshipCache()
*/
- @Override
- public String generateTitle() {
- // TODO Auto-generated method stub
- return null;
+ public boolean isProtectedAuthorshipCache() {
+ return protectedAuthorshipCache;
+ }
+
+ /**
+ * @see #isProtectedAuthorshipCache()
+ * @see #getAuthorshipCache()
+ */
+ public void setProtectedAuthorshipCache(boolean protectedAuthorshipCache) {
+ this.protectedAuthorshipCache = protectedAuthorshipCache;
}
+
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