cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/BotanicalName.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 java.util.Map;
  14
  15 import javax.persistence.Entity;
  16 import javax.xml.bind.annotation.XmlAccessType;
  17 import javax.xml.bind.annotation.XmlAccessorType;
  18 import javax.xml.bind.annotation.XmlElement;
  19 import javax.xml.bind.annotation.XmlRootElement;
  20 import javax.xml.bind.annotation.XmlType;
  21
  22 import org.apache.log4j.Logger;
  23 import org.hibernate.envers.Audited;
  24 import org.hibernate.search.annotations.Indexed;
  25 import org.springframework.beans.factory.annotation.Configurable;
  26
  27 import eu.etaxonomy.cdm.common.CdmUtils;
  28 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  29 import eu.etaxonomy.cdm.model.common.CdmBase;
  30 import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
  31 import eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy;
  32 import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;
  33 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  34
  35 /**
  36  * The taxon name class for plants and fungi.
  37  * <P>
  38  * This class corresponds to: NameBotanical according to the ABCD schema.
  39  *
  40  * @author m.doering
  41  * @version 1.0
  42  * @created 08-Nov-2007 13:06:15
  43  */
  44 @XmlAccessorType(XmlAccessType.FIELD)
  45 @XmlType(name = "BotanicalName", propOrder = {
  46     "anamorphic"
  47 })
  48 @XmlRootElement(name = "BotanicalName")
  49 @Entity
  50 @Indexed(index = "eu.etaxonomy.cdm.model.name.TaxonNameBase")
  51 @Audited
  52 @Configurable
  53 public class BotanicalName extends NonViralName<BotanicalName> implements Cloneable /*, IMergable*/ {
  54         private static final long serialVersionUID = 6818651572463497727L;
  55         @SuppressWarnings("unused")
  56         private static final Logger logger = Logger.getLogger(BotanicalName.class);
  57
  58         //Only for fungi: to indicate that the type of the name is asexual or not
  59     @XmlElement(name ="IsAnamorphic")
  60         private boolean anamorphic;
  61
  62         static private INonViralNameParser<?> nameParser = new NonViralNameParserImpl();
  63
  64         // ************* CONSTRUCTORS *************/
  65         //needed by hibernate
  66         /**
  67          * Class constructor: creates a new botanical taxon name instance
  68          * only containing the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
  69          *
  70          * @see #BotanicalName(Rank, HomotypicalGroup)
  71          * @see #BotanicalName(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
  72          * @see eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
  73          */
  74         protected BotanicalName(){
  75                 super();
  76                 this.cacheStrategy = BotanicNameDefaultCacheStrategy.NewInstance();
  77         }
  78         /**
  79          * Class constructor: creates a new botanical taxon name instance
  80          * only containing its {@link Rank rank},
  81          * its {@link HomotypicalGroup homotypical group} and
  82          * the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
  83          * The new botanical taxon name instance will be also added to the set of
  84          * botanical taxon names belonging to this homotypical group.
  85          *
  86          * @param       rank  the rank to be assigned to <i>this</i> botanical taxon name
  87          * @param       homotypicalGroup  the homotypical group to which <i>this</i> botanical taxon name belongs
  88          * @see         #BotanicalName()
  89          * @see         #BotanicalName(Rank, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
  90          * @see         eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
  91          */
  92         protected BotanicalName(Rank rank, HomotypicalGroup homotypicalGroup) {
  93                 super(rank, homotypicalGroup);
  94                 this.cacheStrategy = BotanicNameDefaultCacheStrategy.NewInstance();
  95         }
  96         /**
  97          * Class constructor: creates a new botanical taxon name instance
  98          * containing its {@link Rank rank},
  99          * its {@link HomotypicalGroup homotypical group},
 100          * its scientific name components, its {@link eu.etaxonomy.cdm.model.agent.TeamOrPersonBase author(team)},
 101          * its {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} and
 102          * the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
 103          * The new botanical taxon name instance will be also added to the set of
 104          * botanical taxon names belonging to this homotypical group.
 105          *
 106          * @param       rank  the rank to be assigned to <i>this</i> botanical taxon name
 107          * @param       genusOrUninomial the string for <i>this</i> botanical taxon name
 108          *                      if its rank is genus or higher or for the genus part
 109          *                      if its rank is lower than genus
 110          * @param       infraGenericEpithet  the string for the first epithet of
 111          *                      <i>this</i> botanical taxon name if its rank is lower than genus
 112          *                      and higher than species aggregate
 113          * @param       specificEpithet  the string for the first epithet of
 114          *                      <i>this</i> botanical taxon name if its rank is species aggregate or lower
 115          * @param       infraSpecificEpithet  the string for the second epithet of
 116          *                      <i>this</i> botanical taxon name if its rank is lower than species
 117          * @param       combinationAuthorTeam  the author or the team who published <i>this</i> botanical taxon name
 118          * @param       nomenclaturalReference  the nomenclatural reference where <i>this</i> botanical taxon name was published
 119          * @param       nomenclMicroRef  the string with the details for precise location within the nomenclatural reference
 120          * @param       homotypicalGroup  the homotypical group to which <i>this</i> botanical taxon name belongs
 121          * @see         #BotanicalName()
 122          * @see         #BotanicalName(Rank, HomotypicalGroup)
 123          * @see         #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
 124          * @see         eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
 125          * @see         eu.etaxonomy.cdm.strategy.cache.name.INonViralNameCacheStrategy
 126          * @see         eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy
 127          */
 128         protected BotanicalName(Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorTeam, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
 129                 super(rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorTeam, nomenclaturalReference, nomenclMicroRef, homotypicalGroup);
 130                 this.cacheStrategy = BotanicNameDefaultCacheStrategy.NewInstance();
 131         }
 132
 133
 134         //********* METHODS **************************************/
 135
 136         /**
 137          * Creates a new botanical taxon name instance
 138          * only containing its {@link Rank rank} and
 139          * the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
 140          *
 141          * @param       rank    the rank to be assigned to <i>this</i> botanical taxon name
 142          * @see                         #BotanicalName(Rank, HomotypicalGroup)
 143          * @see                         #NewInstance(Rank, HomotypicalGroup)
 144          * @see                         #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
 145          * @see                         eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
 146          */
 147         public static BotanicalName NewInstance(Rank rank){
 148                 return new BotanicalName(rank, null);
 149         }
 150         /**
 151          * Creates a new botanical taxon name instance
 152          * only containing its {@link Rank rank},
 153          * its {@link HomotypicalGroup homotypical group} and
 154          * the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
 155          * The new botanical taxon name instance will be also added to the set of
 156          * botanical taxon names belonging to this homotypical group.
 157          *
 158          * @param  rank  the rank to be assigned to <i>this</i> botanical taxon name
 159          * @param  homotypicalGroup  the homotypical group to which <i>this</i> botanical taxon name belongs
 160          * @see    #NewInstance(Rank)
 161          * @see    #NewInstance(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
 162          * @see    #BotanicalName(Rank, HomotypicalGroup)
 163          * @see    eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
 164          */
 165         public static BotanicalName NewInstance(Rank rank, HomotypicalGroup homotypicalGroup){
 166                 return new BotanicalName(rank, homotypicalGroup);
 167         }
 168         /**
 169          * Creates a new botanical taxon name instance
 170          * containing its {@link Rank rank},
 171          * its {@link HomotypicalGroup homotypical group},
 172          * its scientific name components, its {@link eu.etaxonomy.cdm.model.agent.TeamOrPersonBase author(team)},
 173          * its {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference} and
 174          * the {@link eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy default cache strategy}.
 175          * The new botanical taxon name instance will be also added to the set of
 176          * botanical taxon names belonging to this homotypical group.
 177          *
 178          * @param       rank  the rank to be assigned to <i>this</i> botanical taxon name
 179          * @param       genusOrUninomial the string for <i>this</i> botanical 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          *                      <i>this</i> botanical 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          *                      <i>this</i> botanical taxon name if its rank is species aggregate or lower
 187          * @param       infraSpecificEpithet  the string for the second epithet of
 188          *                      <i>this</i> botanical taxon name if its rank is lower than species
 189          * @param       combinationAuthorTeam  the author or the team who published <i>this</i> botanical taxon name
 190          * @param       nomenclaturalReference  the nomenclatural reference where <i>this</i> botanical 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 <i>this</i> botanical taxon name belongs
 193          * @see         #NewInstance(Rank)
 194          * @see         #NewInstance(Rank, HomotypicalGroup)
 195          * @see         ZoologicalName#ZoologicalName(Rank, String, String, String, String, TeamOrPersonBase, INomenclaturalReference, String, HomotypicalGroup)
 196          * @see         eu.etaxonomy.cdm.strategy.cache.name.BotanicNameDefaultCacheStrategy
 197          */
 198         public static  BotanicalName NewInstance(Rank rank, String genusOrUninomial, String infraGenericEpithet, String specificEpithet, String infraSpecificEpithet, TeamOrPersonBase combinationAuthorTeam, INomenclaturalReference nomenclaturalReference, String nomenclMicroRef, HomotypicalGroup homotypicalGroup) {
 199                 return new BotanicalName(rank, genusOrUninomial, infraGenericEpithet, specificEpithet, infraSpecificEpithet, combinationAuthorTeam, nomenclaturalReference, nomenclMicroRef, homotypicalGroup);
 200         }
 201
 202         /**
 203          * Returns a botanical taxon name based on parsing a string representing
 204          * all elements (according to the ICBN) of a botanical taxon name (where
 205          * the scientific name is an uninomial) including authorship but without
 206          * nomenclatural reference. If the {@link Rank rank} is not "Genus" it should be
 207          * set afterwards with the {@link TaxonNameBase#setRank(Rank) setRank} methode.
 208          *
 209          * @param       fullNameString  the string to be parsed
 210          * @return                                      the new botanical taxon name
 211          */
 212         public static BotanicalName PARSED_NAME(String fullNameString){
 213                 return PARSED_NAME(fullNameString, Rank.GENUS());
 214         }
 215
 216         /**
 217          * Returns a botanical taxon name based on parsing a string representing
 218          * all elements (according to the ICBN) of a botanical taxon name including
 219          * authorship but without nomenclatural reference. The parsing result
 220          * depends on the given rank of the botanical 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 botanical taxon name
 225          */
 226         public static BotanicalName PARSED_NAME(String fullNameString, Rank rank){
 227                 if (nameParser == null){
 228                         nameParser = new NonViralNameParserImpl();
 229                 }
 230                 return (BotanicalName)nameParser.parseFullName(fullNameString, NomenclaturalCode.ICNAFP,  rank);
 231         }
 232
 233         /**
 234          * Returns a botanical taxon name based on parsing a string representing
 235          * all elements (according to the ICBN) of a botanical taxon name (where
 236          * the scientific name is an uninomial) including authorship and
 237          * nomenclatural reference. Eventually a new {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference}
 238          * instance will also be created. If the {@link Rank rank} is not "Genus" it should be
 239          * set afterwards with the {@link TaxonNameBase#setRank(Rank) setRank} methode.
 240          *
 241          * @param       fullNameAndReferenceString  the string to be parsed
 242          * @return                                                              the new botanical taxon name
 243          */
 244         public static BotanicalName PARSED_REFERENCE(String fullNameAndReferenceString){
 245                 return PARSED_REFERENCE(fullNameAndReferenceString, Rank.GENUS());
 246         }
 247
 248         /**
 249          * Returns a botanical taxon name based on parsing a string representing
 250          * all elements (according to the ICBN) of a botanical taxon name including
 251          * authorship and nomenclatural reference. The parsing result depends on
 252          * the given rank of the botanical taxon name to be created.
 253          * Eventually a new {@link eu.etaxonomy.cdm.model.reference.INomenclaturalReference nomenclatural reference}
 254          * instance will also be created.
 255          *
 256          * @param       fullNameAndReferenceString  the string to be parsed
 257          * @param   rank                                                the rank of the taxon name
 258          * @return                                                              the new botanical taxon name
 259          */
 260         public static BotanicalName PARSED_REFERENCE(String fullNameAndReferenceString, Rank rank){
 261                 if (nameParser == null){
 262                         nameParser = new NonViralNameParserImpl();
 263                 }
 264                 return (BotanicalName)nameParser.parseReferencedName(fullNameAndReferenceString, NomenclaturalCode.ICNAFP, rank);
 265         }
 266
 267 //***********************
 268
 269         private static Map<String, java.lang.reflect.Field> allFields = null;
 270         @Override
 271     protected Map<String, java.lang.reflect.Field> getAllFields(){
 272         if (allFields == null){
 273                         allFields = CdmUtils.getAllFields(this.getClass(), CdmBase.class, false, false, false, true);
 274                 }
 275         return allFields;
 276     }
 277
 278 //*************************
 279
 280         /**
 281          * Returns the boolean value of the flag indicating whether the specimen
 282          * type of <i>this</i> botanical taxon name for a fungus is asexual (true) or not
 283          * (false). This applies only in case of fungi. The Article 59 of the ICBN
 284          * permits mycologists to give asexually reproducing fungi (anamorphs)
 285          * separate names from their sexual states (teleomorphs).
 286          *
 287          * @return  the boolean value of the isAnamorphic flag
 288          */
 289         public boolean isAnamorphic(){
 290                 return this.anamorphic;
 291         }
 292
 293         /**
 294          * @see  #isAnamorphic()
 295          */
 296         public void setAnamorphic(boolean anamorphic){
 297                 this.anamorphic = anamorphic;
 298         }
 299
 300
 301         /**
 302          * Returns the {@link NomenclaturalCode nomenclatural code} that governs
 303          * the construction of <i>this</i> botanical taxon name, that is the
 304          * International Code of Botanical Nomenclature. This method overrides
 305          * the getNomeclaturalCode method from {@link NonViralName NonViralName}.
 306          *
 307          * @return  the nomenclatural code for plants
 308          * @see         NonViralName#isCodeCompliant()
 309          * @see         TaxonNameBase#getHasProblem()
 310          */
 311         @Override
 312         public NomenclaturalCode getNomenclaturalCode(){
 313                 return NomenclaturalCode.ICNAFP;
 314         }
 315
 316
 317         /**
 318          * Checks if this name is an autonym.<BR>
 319          * An autonym is a taxon name that has equal specific and infra specific epithets.<BR>
 320          * {@link http://ibot.sav.sk/icbn/frameset/0010Ch2Sec1a006.htm#6.8. Vienna Code §6.8}
 321          * or a taxon name that has equal generic and infrageneric epithets (A22.2)
 322          * @return true, if name has Rank, Rank is below species and species epithet equals infraSpeciesEpithtet, else false
 323          */
 324         @Override
 325         public boolean isAutonym(){
 326                 if (this.getRank() != null && this.getSpecificEpithet() != null && this.getInfraSpecificEpithet() != null &&
 327                                 this.getRank().isInfraSpecific() && this.getSpecificEpithet().trim().equals(this.getInfraSpecificEpithet().trim())){
 328                         return true;
 329                 }else if (this.getRank() != null && this.getGenusOrUninomial() != null && this.getInfraGenericEpithet() != null &&
 330                                 this.getRank().isInfraGeneric() && this.getGenusOrUninomial().trim().equals(this.getInfraGenericEpithet().trim())){
 331                         return true;
 332                 }else{
 333                         return false;
 334                 }
 335         }
 336
 337 //*********************** CLONE ********************************************************/
 338
 339         /**
 340          * Clones <i>this</i> botanical name. This is a shortcut that enables to create
 341          * a new instance that differs only slightly from <i>this</i> botanical name by
 342          * modifying only some of the attributes.
 343          *
 344          * @see eu.etaxonomy.cdm.model.name.NonViralName#clone()
 345          * @see java.lang.Object#clone()
 346          */
 347         @Override
 348         public Object clone() {
 349                 BotanicalName result = (BotanicalName)super.clone();
 350                 //no changes to: title, authorTeam, hasProblem, nomenclaturallyRelevant, uri
 351                 return result;
 352         }
 353
 354
 355 }