cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/ZoologicalName.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.model.name;
  11
  12
  13 import javax.persistence.Entity;
  14 import javax.persistence.Transient;
  15
  16 import org.apache.log4j.Logger;
  17
  18 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  19 import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
  20 import eu.etaxonomy.cdm.strategy.cache.name.ZooNameDefaultCacheStrategy;
  21 import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;
  22 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  23
  24 import javax.xml.bind.annotation.XmlAccessType;
  25 import javax.xml.bind.annotation.XmlAccessorType;
  26 import javax.xml.bind.annotation.XmlElement;
  27 import javax.xml.bind.annotation.XmlRootElement;
  28 import javax.xml.bind.annotation.XmlType;
  29
  30 /**
  31  * The taxon name class for animals.
  32  *
  33  * @author m.doering
  34  * @version 1.0
  35  * @created 08-Nov-2007 13:07:03
  36  * @see NonViralName
  37  */
  38 @XmlAccessorType(XmlAccessType.FIELD)
  39 @XmlType(name = "ZoologicalName", propOrder = {
  40     "breed",
  41     "publicationYear",
  42     "originalPublicationYear"
  43 })
  44 @XmlRootElement(name = "ZoologicalName")
  45 @Entity
  46 public class ZoologicalName extends NonViralName {
  47
  48         static Logger logger = Logger.getLogger(ZoologicalName.class);
  49
  50         //Name of the breed of an animal
  51         @XmlElement(name = "Breed")
  52         private String breed;
  53
  54         @XmlElement(name = "PublicationYear")
  55         private Integer publicationYear;
  56
  57         @XmlElement(name = "OriginalPublicationYear")
  58         private Integer originalPublicationYear;
  59
  60         static private INonViralNameParser nameParser = new NonViralNameParserImpl();
  61
  62
  63         // ************* CONSTRUCTORS *************/
  64         /**
  65          * Class constructor: creates a new zoological taxon name instance
  66          * only containing the {@link eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy default cache strategy}.
  67          *
  68          * @see #ZoologicalName(Rank, HomotypicalGroup)
  69          * @see #ZoologicalName(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
  70          * @see eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy
  71          */
  72         protected ZoologicalName() {
  73                 this.cacheStrategy = ZooNameDefaultCacheStrategy.NewInstance();
  74         }
  75
  76         /**
  77          * Class constructor: creates a new zoological taxon name instance
  78          * only containing its {@link common.Rank rank},
  79          * its {@link HomotypicalGroup homotypical group} and
  80          * the {@link eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy default cache strategy}.
  81          * The new zoological taxon name instance will be also added to the set of
  82          * zoological taxon names belonging to this homotypical group.
  83          *
  84          * @param       rank  the rank to be assigned to this zoological taxon name
  85          * @param       homotypicalGroup  the homotypical group to which this zoological taxon name belongs
  86          * @see         #ZoologicalName()
  87          * @see         #ZoologicalName(Rank, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
  88          * @see         eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy
  89          */
  90         protected ZoologicalName(Rank rank, HomotypicalGroup homotypicalGroup) {
  91                 super(rank, homotypicalGroup);
  92                 this.cacheStrategy = ZooNameDefaultCacheStrategy.NewInstance();
  93         }
  94
  95         /**
  96          * Class constructor: creates a new zoological taxon name instance
  97          * containing its {@link common.Rank rank},
  98          * its {@link HomotypicalGroup homotypical group},
  99          * its scientific name components, its {@link agent.TeamOrPersonBase author(team)},
 100          * its {@link reference.INomenclaturalReference nomenclatural reference} and
 101          * the {@link eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy default cache strategy}.
 102          * The new zoological taxon name instance will be also added to the set of
 103          * zoological taxon names belonging to this homotypical group.
 104          *
 105          * @param       rank  the rank to be assigned to this zoological taxon name
 106          * @param       genusOrUninomial the string for this zoological taxon name
 107          *                      if its rank is genus or higher or for the genus part
 108          *                      if its rank is lower than genus
 109          * @param       infraGenericEpithet  the string for the first epithet of
 110          *                      this zoological taxon name if its rank is lower than genus
 111          *                      and higher than species aggregate
 112          * @param       specificEpithet  the string for the first epithet of
 113          *                      this zoological taxon name if its rank is species aggregate or lower
 114          * @param       infraSpecificEpithet  the string for the second epithet of
 115          *                      this zoological taxon name if its rank is lower than species
 116          * @param       combinationAuthorTeam  the author or the team who published this zoological taxon name
 117          * @param       nomenclaturalReference  the nomenclatural reference where this zoological taxon name was published
 118          * @param       nomenclMicroRef  the string with the details for precise location within the nomenclatural reference
 119          * @param       homotypicalGroup  the homotypical group to which this zoological taxon name belongs
 120          * @see         #ZoologicalName()
 121          * @see         #ZoologicalName(Rank, HomotypicalGroup)
 122          * @see         #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
 123          * @see         eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy
 124          * @see         eu.etaxonomy.cdm.strategy.cache.INonViralNameCacheStrategy
 125          * @see         eu.etaxonomy.cdm.strategy.cache.IIdentifiableEntityCacheStrategy
 126          */
 127         protected ZoologicalName (Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorTeam, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
 128                 super(rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorTeam, nomenclaturalReference, nomenclMicroRef, homotypicalGroup);
 129                 this.cacheStrategy = ZooNameDefaultCacheStrategy.NewInstance();
 130         }
 131
 132
 133         //********* METHODS **************************************/
 134
 135         /**
 136          * Creates a new zoological taxon name instance
 137          * only containing its {@link common.Rank rank} and
 138          * the {@link eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy default cache strategy}.
 139          *
 140          * @param       rank    the rank to be assigned to this zoological taxon name
 141          * @see                         #ZoologicalName(Rank, HomotypicalGroup)
 142          * @see                         #NewInstance(Rank, HomotypicalGroup)
 143          * @see                         #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
 144          * @see                         eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy
 145          */
 146         public static ZoologicalName NewInstance(Rank rank){
 147                 return new ZoologicalName(rank, null);
 148         }
 149
 150         /**
 151          * Creates a new zoological taxon name instance
 152          * only containing its {@link common.Rank rank},
 153          * its {@link HomotypicalGroup homotypical group} and
 154          * the {@link eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy default cache strategy}.
 155          * The new zoological taxon name instance will be also added to the set of
 156          * zoological taxon names belonging to this homotypical group.
 157          *
 158          * @param  rank  the rank to be assigned to this zoological taxon name
 159          * @param  homotypicalGroup  the homotypical group to which this zoological taxon name belongs
 160          * @see    #NewInstance(Rank)
 161          * @see    #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
 162          * @see    #ZoologicalName(Rank, HomotypicalGroup)
 163          * @see    eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy
 164          */
 165         public static ZoologicalName NewInstance(Rank rank, HomotypicalGroup homotypicalGroup){
 166                 return new ZoologicalName(rank, homotypicalGroup);
 167         }
 168         /**
 169          * Creates a new zoological taxon name instance
 170          * containing its {@link common.Rank rank},
 171          * its {@link HomotypicalGroup homotypical group},
 172          * its scientific name components, its {@link agent.TeamOrPersonBase author(team)},
 173          * its {@link reference.INomenclaturalReference nomenclatural reference} and
 174          * the {@link eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy default cache strategy}.
 175          * The new zoological taxon name instance will be also added to the set of
 176          * zoological taxon names belonging to this homotypical group.
 177          *
 178          * @param       rank  the rank to be assigned to this zoological taxon name
 179          * @param       genusOrUninomial the string for this zoological taxon name
 180          *                      if its rank is genus or higher or for the genus part
 181          *                      if its rank is lower than genus
 182          * @param       infraGenericEpithet  the string for the first epithet of
 183          *                      this zoological taxon name if its rank is lower than genus
 184          *                      and higher than species aggregate
 185          * @param       specificEpithet  the string for the first epithet of
 186          *                      this zoological taxon name if its rank is species aggregate or lower
 187          * @param       infraSpecificEpithet  the string for the second epithet of
 188          *                      this zoological taxon name if its rank is lower than species
 189          * @param       combinationAuthorTeam  the author or the team who published this zoological taxon name
 190          * @param       nomenclaturalReference  the nomenclatural reference where this zoological taxon name was published
 191          * @param       nomenclMicroRef  the string with the details for precise location within the nomenclatural reference
 192          * @param       homotypicalGroup  the homotypical group to which this zoological taxon name belongs
 193          * @see         #NewInstance(Rank)
 194          * @see         #NewInstance(Rank, HomotypicalGroup)
 195          * @see         #ZoologicalName(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
 196          * @see         eu.etaxonomy.cdm.strategy.cache.ZooNameDefaultCacheStrategy
 197          */
 198         public static ZoologicalName NewInstance(Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorTeam, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
 199                 return new ZoologicalName(rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorTeam, nomenclaturalReference, nomenclMicroRef, homotypicalGroup);
 200         }
 201
 202
 203         /**
 204          * Returns a zoological taxon name based on parsing a string representing
 205          * all elements (according to the ICZN) of a zoological taxon name (where
 206          * the scientific name is an uninomial) including authorship but without
 207          * nomenclatural reference.
 208          *
 209          * @param       fullNameString  the string to be parsed
 210          * @return                                      the new zoological taxon name
 211          */
 212         public static ZoologicalName PARSED_NAME(String fullNameString){
 213                 return PARSED_NAME(fullNameString, Rank.GENUS());
 214         }
 215
 216         /**
 217          * Returns a zoological taxon name based on parsing a string representing
 218          * all elements (according to the ICZN) of a zoological taxon name including
 219          * authorship but without nomenclatural reference. The parsing result
 220          * depends on the given rank of the zoological taxon name to be created.
 221          *
 222          * @param       fullNameString  the string to be parsed
 223          * @param   rank                        the rank of the taxon name
 224          * @return                                      the new zoological taxon name
 225          */
 226         public static ZoologicalName PARSED_NAME(String fullNameString, Rank rank){
 227                 if (nameParser == null){
 228                         nameParser  = new NonViralNameParserImpl();
 229                 }
 230                 return (ZoologicalName)nameParser.parseFullName(fullNameString, NomenclaturalCode.ICZN(), rank);
 231         }
 232
 233         /**
 234          * Returns the {@link NomenclaturalCode nomenclatural code} that governs
 235          * the construction of this zoological taxon name, that is the
 236          * International Code of Zoological Nomenclature. This method overrides
 237          * the getNomeclaturalCode method from {@link NonViralName#getNomeclaturalCode() NonViralName}.
 238          *
 239          * @return  the nomenclatural code for animals
 240          * @see         NonViralName#isCodeCompliant()
 241          * @see         TaxonNameBase#getHasProblem()
 242          */
 243         @Transient
 244         @Override
 245         public NomenclaturalCode getNomenclaturalCode(){
 246                 return NomenclaturalCode.ICZN();
 247         }
 248
 249 /* ***************** GETTER / SETTER ***************************/
 250
 251         /**
 252          * Returns the breed name string for this animal (zoological taxon name).
 253          *
 254          * @return  the string containing the breed name for this zoological taxon name
 255          */
 256         public String getBreed(){
 257                 return this.breed;
 258         }
 259         /**
 260          * @see  #getBreed()
 261          */
 262         public void setBreed(String breed){
 263                 this.breed = breed;
 264         }
 265
 266         /**
 267          * Returns the publication year (as an integer) for this zoological taxon
 268          * name. If the publicationYear attribute is null and a nomenclatural
 269          * reference exists the year could be computed from the
 270          * {@link reference.INomenclaturalReference#getYear() nomenclatural reference}.
 271          *
 272          * @return  the integer representing the publication year for this zoological taxon name
 273          * @see         #getOriginalPublicationYear()
 274          */
 275         public Integer getPublicationYear() {
 276                 return publicationYear;
 277         }
 278         /**
 279          * @see  #getPublicationYear()
 280          */
 281         public void setPublicationYear(Integer publicationYear) {
 282                 this.publicationYear = publicationYear;
 283         }
 284
 285         /**
 286          * Returns the publication year (as an integer) of the original validly
 287          * published species epithet for this zoological taxon name. This only
 288          * applies for zoological taxon names that are no {@link TaxonNameBase#isOriginalCombination() original combinations}.
 289          * If the originalPublicationYear attribute is null the year could be taken
 290          * from the publication year of the corresponding original name (basionym)
 291          * or from the {@link reference.INomenclaturalReference#getYear() nomenclatural reference} of the basionym
 292          * if it exists.
 293          *
 294          * @return  the integer representing the publication year of the original
 295          *                      species epithet corresponding to this zoological taxon name
 296          * @see         #getPublicationYear()
 297          */
 298         public Integer getOriginalPublicationYear() {
 299                 return originalPublicationYear;
 300         }
 301         /**
 302          * @see  #getOriginalPublicationYear()
 303          */
 304         public void setOriginalPublicationYear(Integer originalPublicationYear) {
 305                 this.originalPublicationYear = originalPublicationYear;
 306         }
 307 }