import org.apache.log4j.Logger;
+import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
+import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
+import eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy;
+import eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy;
+
import javax.persistence.*;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
/**
- * use name attribute for the entire virus name! examples see ICTVdb: http://www.
- * ncbi.nlm.nih.gov/ICTVdb/Ictv/vn_indxA.htm
+ * The taxon name class for viral taxa. The scientific name will be stored
+ * as a string (consisting eventually of several words even combined also with
+ * non alphabetical characters) in the inherited {@link common.IdentifiableEntity#setTitleCache(String) titleCache} attribute.
+ * Classification has no influence on the names of viral taxon names and no
+ * viral taxon must be taxonomically included in another viral taxon with
+ * higher rank. For examples see ICTVdb:
+ * http://www.ncbi.nlm.nih.gov/ICTVdb/Ictv/vn_indxA.htm
+ *
* @author m.doering
* @version 1.0
* @created 08-Nov-2007 13:07:02
*/
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+ "cacheStrategy",
+ "acronym"
+})
+@XmlRootElement(name = "ViralName")
@Entity
-public class ViralName extends TaxonNameBase<ViralName> {
- static Logger logger = Logger.getLogger(ViralName.class);
+public class ViralName extends TaxonNameBase<ViralName, INameCacheStrategy> {
+
+ private static final Logger logger = Logger.getLogger(ViralName.class);
- //The accepted acronym for the Virus, e.g. PCV for Peanut Clump Virus
+ @XmlElement(name = "CacheStrategy")
+ protected INameCacheStrategy cacheStrategy;
+ @XmlElement(name = "Acronym")
private String acronym;
+ // ************* CONSTRUCTORS *************/
+ /**
+ * Class constructor: creates a new viral taxon name instance
+ * only containing its {@link common.Rank rank}.
+ *
+ * @param rank the rank to be assigned to this viral taxon name
+ * @see TaxonNameBase#TaxonNameBase(Rank)
+ */
public ViralName(Rank rank) {
super(rank);
}
+ //********* METHODS **************************************/
+
+ /**
+ * Creates a new viral taxon name instance only containing its {@link common.Rank rank}.
+ *
+ * @param rank the rank to be assigned to this viral taxon name
+ * @see #ViralName(Rank)
+ */
+ public static ViralName NewInstance(Rank rank){
+ return new ViralName(rank);
+ }
+
+ /**
+ * Returns the accepted acronym (an assigned abbreviation) string for this
+ * viral taxon name. For instance PCV stays for Peanut Clump Virus.
+ *
+ * @return the string containing the accepted acronym of this viral taxon name
+ */
public String getAcronym(){
return this.acronym;
}
+ /**
+ * @see #getAcronym()
+ */
public void setAcronym(String acronym){
this.acronym = acronym;
}
+ /**
+ * Generates and returns the string with the scientific name of this
+ * viral taxon name. 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 viral taxon name with authorship (and maybe year)
+ * @see common.IdentifiableEntity#generateTitle()
+ * @see common.IdentifiableEntity#getTitleCache()
+ * @see TaxonNameBase#generateTitle()
+ */
@Override
public String generateTitle(){
logger.warn("not yet implemented");
return this.toString();
}
+ /**
+ * Returns the boolean value "true" if the components of this viral taxon name
+ * follow the rules of the corresponding
+ * {@link NomenclaturalCode International Code of Virus Classification and Nomenclature},
+ * "false" otherwise.
+ * This method overrides and implements the isCodeCompliant method from
+ * the abstract {@link TaxonNameBase#isCodeCompliant() TaxonNameBase} class.
+ *
+ * @return the boolean value expressing the compliance of this viral taxon name to its nomenclatural code
+ * @see TaxonNameBase#isCodeCompliant()
+ */
@Override
@Transient
public boolean isCodeCompliant() {
}
+ /**
+ * Returns the {@link NomenclaturalCode nomenclatural code} that governs
+ * the construction of this viral taxon name, that is the
+ * International Code of Virus Classification and Nomenclature.
+ * This method overrides the getNomeclaturalCode method from {@link TaxonNameBase#getNomeclaturalCode() TaxonNameBase}.
+ *
+ * @return the nomenclatural code for viruses
+ * @see #isCodeCompliant()
+ * @see TaxonNameBase#getHasProblem()
+ */
@Transient
@Override
- public NomenclaturalCode getNomeclaturalCode(){
+ public NomenclaturalCode getNomenclaturalCode(){
return NomenclaturalCode.VIRAL();
}
-}
\ No newline at end of file
+
+ /**
+ * Returns the {@link eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy cache strategy} used to generate
+ * several strings corresponding to this viral taxon name.
+ *
+ * @return the cache strategy used for this viral taxon name
+ * @see eu.etaxonomy.cdm.strategy.cache.name.INameCacheStrategy
+ * @see eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
+ */
+ @Transient
+ @Override
+ public INameCacheStrategy getCacheStrategy() {
+ return cacheStrategy;
+ }
+
+
+ /**
+ * @see #getCacheStrategy()
+ */
+ @Override
+ public void setCacheStrategy(INameCacheStrategy cacheStrategy) {
+ this.cacheStrategy = cacheStrategy;
+ }
+
+}
BGBM BDI Projects / cdmlib.git / blobdiff