cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/name/Rank.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 import javax.xml.bind.annotation.XmlAccessType;
  13 import javax.xml.bind.annotation.XmlAccessorType;
  14 import javax.xml.bind.annotation.XmlType;
  15 import eu.etaxonomy.cdm.model.common.OrderedTermBase;
  16 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  17 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  18
  19 import org.apache.log4j.Logger;
  20 import org.hibernate.envers.Audited;
  21
  22 import java.util.*;
  23
  24 import javax.persistence.*;
  25
  26 /**
  27  * The class representing the taxonomical ranks (like "Family", "Genus" or
  28  * "Species") used for {@link TaxonNameBase taxon names} across all {@link NomenclaturalCode nomenclatural codes}
  29  * for bacteria (ICNB), viruses (ICVCN), plants and fungi (ICBN),
  30  * cultivars (ICNCP) and animals (ICZN).
  31  * <P>
  32  * A standard (ordered) list of taxonomical rank instances will be automatically
  33  * created as the project starts. But this class allows to extend this standard
  34  * list by creating new instances of additional taxonomical ranks if needed.
  35  * <P>
  36  * This class corresponds to: <ul>
  37  * <li> TaxonRankTerm according to the TDWG ontology
  38  * <li> TaxonomicRankEnum according to the TCS
  39  * <li> Rank according to the ABCD schema
  40  * </ul>
  41  *
  42  * @author m.doering
  43  * @version 1.0
  44  * @created 08-Nov-2007 13:06:46
  45  */
  46 @XmlAccessorType(XmlAccessType.FIELD)
  47 @XmlType(name = "Rank")
  48 @Entity
  49 @Audited
  50 public class Rank extends OrderedTermBase<Rank> {
  51         private static final Logger logger = Logger.getLogger(Rank.class);
  52
  53         private static final UUID uuidEmpire = UUID.fromString("ac470211-1586-4b24-95ca-1038050b618d");
  54         private static final UUID uuidDomain = UUID.fromString("ffca6ec8-8b88-417b-a6a0-f7c992aac19b");
  55         private static final UUID uuidSuperkingdom = UUID.fromString("64223610-7625-4cfd-83ad-b797bf7f0edd");
  56         private static final UUID uuidKingdom = UUID.fromString("fbe7109d-66b3-498c-a697-c6c49c686162");
  57         private static final UUID uuidSubkingdom = UUID.fromString("a71bd9d8-f3ab-4083-afb5-d89315d71655");
  58         private static final UUID uuidInfrakingdom = UUID.fromString("1e37930c-86cf-44f6-90fd-7822928df260");
  59         private static final UUID uuidSuperphylum = UUID.fromString("0d0cecb1-e254-4607-b210-6801e7ecbb04");
  60         private static final UUID uuidPhylum = UUID.fromString("773430d2-76b4-438c-b817-97a543a33287");
  61         private static final UUID uuidSubphylum = UUID.fromString("23a9b6ff-9408-49c9-bd9e-7a2ca5ab4725");
  62         private static final UUID uuidInfraphylum = UUID.fromString("1701de3a-7693-42a5-a2d3-42697f944190");
  63         private static final UUID uuidSuperdivision = UUID.fromString("a735a48f-4fc8-49a7-ae0c-6a984f658131");
  64         private static final UUID uuidDivision = UUID.fromString("7e56f5cc-123a-4fd1-8cbb-6fd80358b581");
  65         private static final UUID uuidSubdivision = UUID.fromString("931c840f-7a6b-4d76-ad38-bfdd77d7b2e8");
  66         private static final UUID uuidInfradivision = UUID.fromString("c0ede273-be52-4dee-b411-66ee08d30c94");
  67         private static final UUID uuidSuperclass = UUID.fromString("e65b4e1a-21ec-428d-9b9f-e87721ab967c");
  68         private static final UUID uuidClass = UUID.fromString("f23d14c4-1d34-4ee6-8b4e-eee2eb9a3daf");
  69         private static final UUID uuidSubclass = UUID.fromString("8cb26733-e2f5-46cb-ab5c-f99254f877aa");
  70         private static final UUID uuidInfraclass = UUID.fromString("ad23cfda-879a-4021-8629-c54d27caf717");
  71         private static final UUID uuidSuperorder = UUID.fromString("c8c67a22-301a-4219-b882-4a49121232ff");
  72         private static final UUID uuidOrder = UUID.fromString("b0785a65-c1c1-4eb4-88c7-dbd3df5aaad1");
  73         private static final UUID uuidSuborder = UUID.fromString("768ad378-fa85-42ab-b668-763225832f57");
  74         private static final UUID uuidInfraorder = UUID.fromString("84099182-a6f5-47d7-8586-33c9e9955a10");
  75         private static final UUID uuidSuperfamily = UUID.fromString("2cfa510a-dcea-4a03-b66a-b1528f9b0796");
  76         private static final UUID uuidFamily = UUID.fromString("af5f2481-3192-403f-ae65-7c957a0f02b6");
  77         private static final UUID uuidSubfamily = UUID.fromString("862526ee-7592-4760-a23a-4ff3641541c5");
  78         private static final UUID uuidInfrafamily = UUID.fromString("c3f2e3bb-6eef-4a26-9fb7-b14f4c8c5e4f");
  79         private static final UUID uuidSupertribe = UUID.fromString("11e94828-8c61-499b-87d6-1de35ce2c51c");
  80         private static final UUID uuidTribe = UUID.fromString("4aa6890b-0363-4899-8d7c-ee0cb78e6166");
  81         private static final UUID uuidSubtribe = UUID.fromString("ae41ecc5-5165-4126-9d24-79939ae5d822");
  82         private static final UUID uuidInfratribe = UUID.fromString("1ec02e8f-f2b7-4c65-af9f-b436b34c79a3");
  83         private static final UUID uuidSupragenericTaxon = UUID.fromString("1fdc0b93-c354-441a-8406-091e0303ff5c");
  84         private static final UUID uuidGenus = UUID.fromString("1b11c34c-48a8-4efa-98d5-84f7f66ef43a");
  85         private static final UUID uuidSubgenus = UUID.fromString("78786e16-2a70-48af-a608-494023b91904");
  86         private static final UUID uuidInfragenus = UUID.fromString("a9972969-82cd-4d54-b693-a096422f13fa");
  87         private static final UUID uuidSection = UUID.fromString("3edff68f-8527-49b5-bf91-7e4398bb975c");
  88         private static final UUID uuidSubsection = UUID.fromString("d20f5b61-d463-4448-8f8a-c1ff1f262f59");
  89         private static final UUID uuidSeries = UUID.fromString("d7381ecf-48f8-429b-9c54-f461656978cd");
  90         private static final UUID uuidSubseries = UUID.fromString("80c9a263-f4db-4a13-b6c2-b7fec1aa1200");
  91         private static final UUID uuidSpeciesAggregate = UUID.fromString("1ecae058-4217-4f75-9c27-6d8ba099ac7a");
  92         private static final UUID uuidInfragenericTaxon = UUID.fromString("41bcc6ac-37d3-4fd4-bb80-3cc5b04298b9");
  93         private static final UUID uuidSpecies = UUID.fromString("b301f787-f319-4ccc-a10f-b4ed3b99a86d");
  94         private static final UUID uuidSubspecificAggregate = UUID.fromString("72c248b9-027d-4402-b375-dd4f0850c9ad");
  95         private static final UUID uuidSubspecies = UUID.fromString("462a7819-8b00-4190-8313-88b5be81fad5");
  96         private static final UUID uuidInfraspecies = UUID.fromString("f28ebc9e-bd50-4194-9af1-42f5cb971a2c");
  97         private static final UUID uuidVariety = UUID.fromString("d5feb6a5-af5c-45ef-9878-bb4f36aaf490");
  98         private static final UUID uuidBioVariety = UUID.fromString("a3a364cb-1a92-43fc-a717-3c44980a0991");
  99         private static final UUID uuidPathoVariety = UUID.fromString("2f4f4303-a099-47e3-9048-d749d735423b");
 100         private static final UUID uuidSubvariety = UUID.fromString("9a83862a-7aee-480c-a98d-4bceaf8712ca");
 101         private static final UUID uuidSubsubvariety = UUID.fromString("bff22f84-553a-4429-a4e7-c4b3796c3a18");
 102         private static final UUID uuidConvar = UUID.fromString("2cc740c9-cebb-43c8-9b06-1bef79e6a56a");
 103         private static final UUID uuidForm = UUID.fromString("0461281e-458a-47b9-8d41-19a3d39356d5");
 104         private static final UUID uuidSpecialForm = UUID.fromString("bed20aee-2f5a-4635-9c02-eff06246d067");
 105         private static final UUID uuidSubform = UUID.fromString("47cfc5b0-0fb7-4ceb-b61d-e1dd8de8b569");
 106         private static final UUID uuidSubsubform = UUID.fromString("1c8ac389-4349-4ae0-87be-7239f6635068");
 107         private static final UUID uuidInfraspecificTaxon = UUID.fromString("eb75c27d-e154-4570-9d96-227b2df60474");
 108         private static final UUID uuidCandidate = UUID.fromString("ead9a1f5-dfd4-4de2-9121-70a47accb10b");
 109         private static final UUID uuidDenominationClass = UUID.fromString("49bdf74a-2170-40ed-8be2-887a0db517bf");
 110         private static final UUID uuidGrex = UUID.fromString("08dcb4ff-ac58-48a3-93af-efb3d836ac84");
 111         private static final UUID uuidGraftChimaera = UUID.fromString("6b4063bc-f934-4796-9bf3-0ef3aea5c1cb");
 112         private static final UUID uuidCultivarGroup = UUID.fromString("d763e7d3-e7de-4bb1-9d75-225ca6948659");
 113         private static final UUID uuidCultivar = UUID.fromString("5e98415b-dc6e-440b-95d6-ea33dbb39ad0");
 114         private static final UUID uuidUnknownRank = UUID.fromString("5c4d6755-2cf6-44ca-9220-cccf8881700b");
 115
 116         private static Rank UNKNOWN_RANK;
 117         private static Rank CULTIVAR;
 118         private static Rank CULTIVARGROUP;
 119         private static Rank GRAFTCHIMAERA;
 120         private static Rank GREX;
 121         private static Rank DENOMINATIONCLASS;
 122         private static Rank CANDIDATE;
 123         private static Rank INFRASPECIFICTAXON;
 124         private static Rank SUBSUBFORM;
 125         private static Rank SUBFORM;
 126         private static Rank SPECIALFORM;
 127         private static Rank FORM;
 128         private static Rank CONVAR;
 129         private static Rank SUBSUBVARIETY;
 130         private static Rank SUBVARIETY;
 131         private static Rank PATHOVARIETY;
 132         private static Rank BIOVARIETY;
 133         private static Rank VARIETY;
 134         private static Rank INFRASPECIES;
 135         private static Rank SUBSPECIES;
 136         private static Rank SUBSPECIFICAGGREGATE;
 137         private static Rank SPECIES;
 138         private static Rank INFRAGENERICTAXON;
 139         private static Rank SPECIESAGGREGATE;
 140         private static Rank SUBSERIES;
 141         private static Rank SERIES;
 142         private static Rank SUBSECTION;
 143         private static Rank SECTION;
 144         private static Rank INFRAGENUS;
 145         private static Rank SUBGENUS;
 146         private static Rank GENUS;
 147         private static Rank SUPRAGENERICTAXON;
 148         private static Rank INFRATRIBE;
 149         private static Rank SUBTRIBE;
 150         private static Rank TRIBE;
 151         private static Rank SUPERTRIBE;
 152         private static Rank INFRAFAMILY;
 153         private static Rank SUBFAMILY;
 154         private static Rank FAMILY;
 155         private static Rank SUPERFAMILY;
 156         private static Rank INFRAORDER;
 157         private static Rank SUBORDER;
 158         private static Rank ORDER;
 159         private static Rank SUPERORDER;
 160         private static Rank INFRACLASS;
 161         private static Rank SUBCLASS;
 162         private static Rank CLASS;
 163         private static Rank SUPERCLASS;
 164         private static Rank INFRADIVISION;
 165         private static Rank SUBDIVISION;
 166         private static Rank DIVISION;
 167         private static Rank SUPERDIVISION;
 168         private static Rank INFRAPHYLUM;
 169         private static Rank SUBPHYLUM;
 170         private static Rank PHYLUM;
 171         private static Rank SUPERPHYLUM;
 172         private static Rank INFRAKINGDOM;
 173         private static Rank SUBKINGDOM;
 174         private static Rank KINGDOM;
 175         private static Rank SUPERKINGDOM;
 176         private static Rank DOMAIN;
 177         private static Rank EMPIRE;
 178
 179         // ************* CONSTRUCTORS *************/
 180         /**
 181          * Class constructor: creates a new empty rank instance.
 182          *
 183          * @see         #Rank(String, String, String)
 184          */
 185         public Rank() {
 186         }
 187
 188         /**
 189          * Class constructor: creates an additional rank instance with a description
 190          * (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label and a label abbreviation.
 191          *
 192          * @param       term             the string (in the default language) describing the
 193          *                                               new rank to be created
 194          * @param       label            the string identifying the new rank to be created
 195          * @param       labelAbbrev  the string identifying (in abbreviated form) the
 196          *                                               new rank to be created
 197          * @see         #Rank()
 198          */
 199         public Rank(String term, String label, String labelAbbrev) {
 200                 super(term, label, labelAbbrev);
 201         }
 202
 203         //********* METHODS **************************************/
 204
 205         public static final Rank EMPIRE(){
 206           return EMPIRE;
 207         }
 208         public static final Rank DOMAIN(){
 209           return DOMAIN;
 210         }
 211         public static final Rank SUPERKINGDOM(){
 212           return SUPERKINGDOM;
 213         }
 214         public static final Rank KINGDOM(){
 215           return KINGDOM;
 216         }
 217         public static final Rank SUBKINGDOM(){
 218           return SUBKINGDOM;
 219         }
 220         public static final Rank INFRAKINGDOM(){
 221           return INFRAKINGDOM;
 222         }
 223         public static final Rank SUPERPHYLUM(){
 224           return SUPERPHYLUM;
 225         }
 226         public static final Rank PHYLUM(){
 227           return PHYLUM;
 228         }
 229         public static final Rank SUBPHYLUM(){
 230           return SUBPHYLUM;
 231         }
 232         public static final Rank INFRAPHYLUM(){
 233           return INFRAPHYLUM;
 234         }
 235         public static final Rank SUPERDIVISION(){
 236           return SUPERDIVISION;
 237         }
 238         public static final Rank DIVISION(){
 239           return DIVISION;
 240         }
 241         public static final Rank SUBDIVISION(){
 242           return SUBDIVISION;
 243         }
 244         public static final Rank INFRADIVISION(){
 245           return INFRADIVISION;
 246         }
 247         public static final Rank SUPERCLASS(){
 248           return SUPERCLASS;
 249         }
 250         public static final Rank CLASS(){
 251           return CLASS;
 252         }
 253         public static final Rank SUBCLASS(){
 254           return SUBCLASS;
 255         }
 256         public static final Rank INFRACLASS(){
 257           return INFRACLASS;
 258         }
 259         public static final Rank SUPERORDER(){
 260           return SUPERORDER;
 261         }
 262         public static final Rank ORDER(){
 263           return ORDER;
 264         }
 265         public static final Rank SUBORDER(){
 266           return SUBORDER;
 267         }
 268         public static final Rank INFRAORDER(){
 269           return INFRAORDER;
 270         }
 271         public static final Rank SUPERFAMILY(){
 272           return SUPERFAMILY;
 273         }
 274         public static final Rank FAMILY(){
 275           return FAMILY;
 276         }
 277         public static final Rank SUBFAMILY(){
 278           return SUBFAMILY;
 279         }
 280         public static final Rank INFRAFAMILY(){
 281           return INFRAFAMILY;
 282         }
 283         public static final Rank SUPERTRIBE(){
 284           return SUPERTRIBE;
 285         }
 286         public static final Rank TRIBE(){
 287           return TRIBE;
 288         }
 289         public static final Rank SUBTRIBE(){
 290           return SUBTRIBE;
 291         }
 292         public static final Rank INFRATRIBE(){
 293           return INFRATRIBE;
 294         }
 295         public static final Rank SUPRAGENERICTAXON(){
 296           return SUPRAGENERICTAXON;
 297         }
 298         public static final Rank GENUS(){
 299           return GENUS;
 300         }
 301         public static final Rank SUBGENUS(){
 302           return SUBGENUS;
 303         }
 304         public static final Rank INFRAGENUS(){
 305           return INFRAGENUS;
 306         }
 307         public static final Rank SECTION(){
 308           return SECTION;
 309         }
 310         public static final Rank SUBSECTION(){
 311           return SUBSECTION;
 312         }
 313         public static final Rank SERIES(){
 314           return SERIES;
 315         }
 316         public static final Rank SUBSERIES(){
 317           return SUBSERIES;
 318         }
 319         public static final Rank SPECIESAGGREGATE(){
 320           return SPECIESAGGREGATE;
 321         }
 322         public static final Rank INFRAGENERICTAXON(){
 323           return INFRAGENERICTAXON;
 324         }
 325         public static final Rank SPECIES(){
 326           return SPECIES;
 327         }
 328         public static final Rank SUBSPECIFICAGGREGATE(){
 329           return SUBSPECIFICAGGREGATE;
 330         }
 331         public static final Rank SUBSPECIES(){
 332           return SUBSPECIES;
 333         }
 334         public static final Rank INFRASPECIES(){
 335           return INFRASPECIES;
 336         }
 337         public static final Rank VARIETY(){
 338           return VARIETY;
 339         }
 340         public static final Rank BIOVARIETY(){
 341           return BIOVARIETY;
 342         }
 343         public static final Rank PATHOVARIETY(){
 344           return PATHOVARIETY;
 345         }
 346         public static final Rank SUBVARIETY(){
 347           return SUBVARIETY;
 348         }
 349         public static final Rank SUBSUBVARIETY(){
 350           return SUBSUBVARIETY;
 351         }
 352         public static final Rank CONVAR(){
 353           return CONVAR;
 354         }
 355         public static final Rank FORM(){
 356           return FORM;
 357         }
 358         public static final Rank SPECIALFORM(){
 359           return SPECIALFORM;
 360         }
 361         public static final Rank SUBFORM(){
 362           return SUBFORM;
 363         }
 364         public static final Rank SUBSUBFORM(){
 365           return SUBSUBFORM;
 366         }
 367         public static final Rank INFRASPECIFICTAXON(){
 368           return INFRASPECIFICTAXON;
 369         }
 370         public static final Rank CANDIDATE(){
 371           return CANDIDATE;
 372         }
 373         public static final Rank DENOMINATIONCLASS(){
 374           return DENOMINATIONCLASS;
 375         }
 376         public static final Rank GREX(){
 377           return GREX;
 378         }
 379         public static final Rank GRAFTCHIMAERA(){
 380           return GRAFTCHIMAERA;
 381         }
 382         public static final Rank CULTIVARGROUP(){
 383           return CULTIVARGROUP;
 384         }
 385         public static final Rank CULTIVAR(){
 386           return CULTIVAR;
 387         }
 388         public static final Rank UNKNOWN_RANK(){
 389                   return UNKNOWN_RANK;
 390         }
 391
 392         /**
 393          * Returns the boolean value indicating whether <i>this</i> rank is higher than
 394          * the genus rank (true) or not (false). Returns false if <i>this</i> rank is null.
 395          *
 396          * @see  #isGenus()
 397          * @see  #isInfraGeneric()
 398          * @see  #isSpecies()
 399          * @see  #isInfraSpecific()
 400          */
 401         @Transient
 402         public boolean isSupraGeneric(){
 403                 return (this.isHigher(Rank.GENUS()));
 404         }
 405
 406         /**
 407          * Returns the boolean value indicating whether <i>this</i> rank is the genus rank
 408          * (true) or not (false). Returns false if <i>this</i> rank is null.
 409          *
 410          * @see  #isSupraGeneric()
 411          * @see  #isInfraGeneric()
 412          * @see  #isSpecies()
 413          * @see  #isInfraSpecific()
 414          */
 415         @Transient
 416         public boolean isGenus(){
 417                 return (this.equals(Rank.GENUS()));
 418         }
 419
 420         /**
 421          * Returns the boolean value indicating whether <i>this</i> rank is higher than the
 422          * species rank and lower than the genus rank (true) or not (false).
 423          * Returns false if <i>this</i> rank is null.
 424          *
 425          * @see  #isSupraGeneric()
 426          * @see  #isGenus()
 427          * @see  #isSpecies()
 428          * @see  #isInfraSpecific()
 429          */
 430         @Transient
 431         public boolean isInfraGeneric(){
 432                 return (this.isLower(Rank.GENUS()) && this.isHigher(Rank.SPECIES()));
 433         }
 434
 435         /**
 436          * Returns the boolean value indicating whether <i>this</i> rank is the species
 437          * rank (true) or not (false). Returns false if <i>this</i> rank is null.
 438          *
 439          * @see  #isSupraGeneric()
 440          * @see  #isGenus()
 441          * @see  #isInfraGeneric()
 442          * @see  #isInfraSpecific()
 443          */
 444         @Transient
 445         public boolean isSpecies(){
 446                 return (this.equals(Rank.SPECIES()));
 447         }
 448
 449         /**
 450          * Returns the boolean value indicating whether <i>this</i> rank is lower than the
 451          * species rank (true) or not (false). Returns false if <i>this</i> rank is null.
 452          *
 453          * @see  #isSupraGeneric()
 454          * @see  #isGenus()
 455          * @see  #isInfraGeneric()
 456          * @see  #isSpecies()
 457          */
 458         @Transient
 459         public boolean isInfraSpecific(){
 460                 return (this.isLower(Rank.SPECIES()));
 461         }
 462
 463
 464         /**
 465          * Returns the rank identified through a name (abbreviated or not).
 466          * Preliminary implementation for BotanicalNameParser.
 467          *
 468          * @param       strRank the string identifying the rank
 469          * @return              the rank
 470          */
 471         public static Rank getRankByNameOrAbbreviation(String strRank)
 472                                 throws UnknownCdmTypeException{
 473                 return getRankByNameOrAbbreviation(strRank, false);
 474         }
 475
 476         // TODO
 477         // Preliminary implementation for BotanicalNameParser.
 478         // not yet complete
 479         /**
 480          * Returns the rank identified through a name (abbreviated or not).
 481          * Preliminary implementation for BotanicalNameParser.
 482          *
 483          * @param       strRank the string identifying the rank
 484          * @param       useUnknown      if true the rank UNKNOWN_RANK is returned if the abbrev is
 485          *                      unknown or not yet implemented
 486          * @return              the rank
 487          */
 488         public static Rank getRankByNameOrAbbreviation(String strRank, boolean useUnknown)
 489                         throws UnknownCdmTypeException{
 490                 try {
 491                         return getRankByAbbreviation(strRank);
 492                 } catch (UnknownCdmTypeException e) {
 493                         return getRankByName(strRank, useUnknown);
 494                 }
 495         }
 496
 497
 498         /**
 499          * Returns the rank identified through an abbreviated name.
 500          * Preliminary implementation for BotanicalNameParser.
 501          *
 502          * @param       abbrev  the string for the name abbreviation
 503          * @return              the rank
 504          */
 505         public static Rank getRankByAbbreviation(String abbrev)
 506                                                 throws UnknownCdmTypeException{
 507                 return getRankByAbbreviation(abbrev, false);
 508         }
 509
 510         // TODO
 511         // Preliminary implementation for BotanicalNameParser.
 512         // not yet complete
 513         /**
 514          * Returns the rank identified through an abbreviated name.
 515          * Preliminary implementation for BotanicalNameParser.
 516          *
 517          * @param       abbrev          the string for the name abbreviation
 518          * @param       useUnknown      if true the rank UNKNOWN_RANK is returned if the abbrev is
 519          *                      unknown or not yet implemented
 520          * @return  the rank
 521          */
 522         public static Rank getRankByAbbreviation(String abbrev, boolean useUnknown)
 523                                                 throws UnknownCdmTypeException{
 524                 if (abbrev == null){ throw new NullPointerException("abbrev is 'null' in getRankByAbbreviation");
 525                 }else if (abbrev.equalsIgnoreCase("reg.")){     return Rank.KINGDOM();
 526                 }else if (abbrev.equalsIgnoreCase("subreg.")){ return Rank.SUBKINGDOM();
 527                 }else if (abbrev.equalsIgnoreCase("phyl.")){return Rank.PHYLUM();
 528                 }else if (abbrev.equalsIgnoreCase("subphyl.")) { return Rank.SUBPHYLUM();
 529                 }else if (abbrev.equalsIgnoreCase("div.")) { return Rank.DIVISION();
 530                 }else if (abbrev.equalsIgnoreCase("subdiv.")) { return Rank.SUBDIVISION();
 531                 }else if (abbrev.equalsIgnoreCase("cl.")) { return Rank.CLASS();
 532                 }else if (abbrev.equalsIgnoreCase("subcl.")) { return Rank.SUBCLASS();
 533                 }else if (abbrev.equalsIgnoreCase("superor.")) { return Rank.SUPERORDER();
 534                 }else if (abbrev.equalsIgnoreCase("ordo")) { return Rank.ORDER();
 535                 }else if (abbrev.equalsIgnoreCase("subor.")) { return Rank.SUBORDER();
 536                 }else if (abbrev.equalsIgnoreCase("fam.")) { return Rank.FAMILY();
 537                 }else if (abbrev.equalsIgnoreCase("subfam.")) { return Rank.SUBFAMILY();
 538                 }else if (abbrev.equalsIgnoreCase("trib.")) { return Rank.TRIBE();
 539                 }else if (abbrev.equalsIgnoreCase("subtrib.")) { return Rank.SUBTRIBE();
 540                 }else if (abbrev.equalsIgnoreCase("gen.")) { return Rank.GENUS();
 541                 }else if (abbrev.equalsIgnoreCase("subg.")) { return Rank.SUBGENUS();
 542                 }else if (abbrev.equalsIgnoreCase("sect.")) { return Rank.SECTION();
 543                 }else if (abbrev.equalsIgnoreCase("subsect.")) { return Rank.SUBSECTION();
 544                 }else if (abbrev.equalsIgnoreCase("ser.")) { return Rank.SERIES();
 545                 }else if (abbrev.equalsIgnoreCase("subser.")) { return Rank.SUBSERIES();
 546                 }else if (abbrev.equalsIgnoreCase("aggr.")) { return Rank.SPECIESAGGREGATE();
 547                 //TODO
 548                 //}else if (abbrev.equalsIgnoreCase("group")) { return Rank.SPECIESGROUP();
 549                 }else if (abbrev.equalsIgnoreCase("sp.")) { return Rank.SPECIES();
 550                 }else if (abbrev.equalsIgnoreCase("subsp.")) { return Rank.SUBSPECIES();
 551                 }else if (abbrev.equalsIgnoreCase("convar.")) { return Rank.CONVAR();
 552                 }else if (abbrev.equalsIgnoreCase("var.")) { return Rank.VARIETY();
 553                 }else if (abbrev.equalsIgnoreCase("subvar.")) { return Rank.SUBVARIETY();
 554                 }else if (abbrev.equalsIgnoreCase("f.")) { return Rank.FORM();
 555                 }else if (abbrev.equalsIgnoreCase("subf.")) { return Rank.SUBFORM();
 556                 //TODO
 557                 //}else if (abbrev.equalsIgnoreCase("f.spec.")) { return Rank.FORMA_SPEC();
 558                 }else if (abbrev.equalsIgnoreCase("t.infgen.")) { return Rank.INFRAGENERICTAXON();
 559                 }else if (abbrev.equalsIgnoreCase("t.infr.")) { return Rank.INFRASPECIFICTAXON();
 560                 }else {
 561                         if (abbrev == null){
 562                                 abbrev = "(null)";
 563                         }
 564                         if (useUnknown){
 565                                 logger.info("Unknown rank name: " + abbrev+". Rank 'UNKNOWN_RANK' created instead");
 566                                 return Rank.UNKNOWN_RANK();
 567                         }else{
 568                                 if (abbrev == null){
 569                                         abbrev = "(null)";
 570                                 }
 571                                 throw new UnknownCdmTypeException("Unknown rank abbreviation: " + abbrev);
 572                         }
 573                 }
 574         }
 575
 576         // TODO
 577         // Preliminary implementation for BotanicalNameParser.
 578         // not yet complete
 579         /**
 580          * Returns the rank identified through a name.
 581          * Preliminary implementation for BotanicalNameParser.
 582          *
 583          * @param       rankName        the string for the name of the rank
 584          * @return                      the rank
 585          */
 586         public static Rank getRankByName(String rankName)throws UnknownCdmTypeException{
 587                 return getRankByName(rankName, false);
 588         }
 589
 590
 591         /**
 592          * Returns the rank identified through a name.
 593          * Preliminary implementation for BotanicalNameParser.
 594          *
 595          * @param       rankName        the string for the name of the rank
 596          * @param       useUnknown      if true the rank UNKNOWN_RANK is returned if the rank name is
 597          *                      unknown or not yet implemented
 598          * @return                      the rank
 599          */
 600         public static Rank getRankByName(String rankName, boolean useUnknown)
 601                         throws UnknownCdmTypeException{
 602                 if (rankName.equalsIgnoreCase("Regnum")){ return Rank.KINGDOM();
 603                 }else if (rankName.equalsIgnoreCase("Subregnum")){ return Rank.SUBKINGDOM();
 604                 }else if (rankName.equalsIgnoreCase("Phylum")){ return Rank.PHYLUM();
 605                 }else if (rankName.equalsIgnoreCase("subphylum")){ return Rank.SUBPHYLUM();
 606                 }else if (rankName.equalsIgnoreCase("Divisio")){ return Rank.DIVISION();
 607                 }else if (rankName.equalsIgnoreCase("Subdivisio")){ return Rank.SUBDIVISION();
 608                 }else if (rankName.equalsIgnoreCase("Classis")){ return Rank.CLASS();
 609                 }else if (rankName.equalsIgnoreCase("Subclassis")){ return Rank.SUBCLASS();
 610                 }else if (rankName.equalsIgnoreCase("Superordo")){ return Rank.SUPERORDER();
 611                 }else if (rankName.equalsIgnoreCase("Ordo")){ return Rank.ORDER();
 612                 }else if (rankName.equalsIgnoreCase("Subordo")){ return Rank.SUBORDER();
 613                 }else if (rankName.equalsIgnoreCase("Familia")){ return Rank.FAMILY();
 614                 }else if (rankName.equalsIgnoreCase("Subfamilia")){ return Rank.SUBFAMILY();
 615                 }else if (rankName.equalsIgnoreCase("Tribus")){ return Rank.TRIBE();
 616                 }else if (rankName.equalsIgnoreCase("Subtribus")){ return Rank.SUBTRIBE();
 617                 }else if (rankName.equalsIgnoreCase("Genus")){ return Rank.GENUS();
 618                 }else if (rankName.equalsIgnoreCase("Subgenus")){ return Rank.SUBGENUS();
 619                 }else if (rankName.equalsIgnoreCase("Sectio")){ return Rank.SECTION();
 620                 }else if (rankName.equalsIgnoreCase("Subsectio")){ return Rank.SUBSECTION();
 621                 }else if (rankName.equalsIgnoreCase("Series")){ return Rank.SERIES();
 622                 }else if (rankName.equalsIgnoreCase("Subseries")){ return Rank.SUBSERIES();
 623                 }else if (rankName.equalsIgnoreCase("Aggregate")){ return Rank.SPECIESAGGREGATE();
 624                 //TODO
 625                 //}else if (rankName.equalsIgnoreCase("Speciesgroup")){ return Rank.SPECIESGROUP();
 626                 }else if (rankName.equalsIgnoreCase("Species")){ return Rank.SPECIES();
 627                 }else if (rankName.equalsIgnoreCase("Subspecies")){ return Rank.SUBSPECIES();
 628                 }else if (rankName.equalsIgnoreCase("Convarietas")){ return Rank.CONVAR();
 629                 }else if (rankName.equalsIgnoreCase("Varietas")){ return Rank.VARIETY();
 630                 }else if (rankName.equalsIgnoreCase("Subvarietas")){ return Rank.SUBVARIETY();
 631                 }else if (rankName.equalsIgnoreCase("Forma")){ return Rank.FORM();
 632                 }else if (rankName.equalsIgnoreCase("Subforma")){ return Rank.SUBFORM();
 633                 }else if (rankName.equalsIgnoreCase("Forma spec.")){ return Rank.SPECIALFORM();
 634                 }else if (rankName.equalsIgnoreCase("tax.infragen.")){ return Rank.INFRAGENERICTAXON();
 635                 }else if (rankName.equalsIgnoreCase("tax.infrasp.")){ return Rank.INFRASPECIFICTAXON();
 636                 // old ranks
 637                 }else if (rankName.equalsIgnoreCase("proles")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
 638                 }else if (rankName.equalsIgnoreCase("race")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
 639                 }else if (rankName.equalsIgnoreCase("taxon")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
 640                 }else if (rankName.equalsIgnoreCase("sublusus")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
 641
 642                 }else{
 643                         if (rankName == null){
 644                                 rankName = "(null)";
 645                         }
 646                         if (useUnknown){
 647                                 logger.info("Unknown rank name: " + rankName+". Rank 'UNKNOWN_RANK' created instead");
 648                                 return Rank.UNKNOWN_RANK();
 649                         }else{
 650                                 if (rankName == null){
 651                                         rankName = "(null)";
 652                                 }
 653                                 throw new UnknownCdmTypeException("Unknown rank name: " + rankName);
 654                         }
 655                 }
 656         }
 657
 658         //TODO
 659         //dummy implementation for BerlinModelImport
 660         // not yet complete
 661         /**
 662          * Returns the abbreviated rank name for <i>this</i> rank according to the
 663          * Berlin Model. Preliminary implementation for BerlinModelImport.
 664          *
 665          * @return      the abbreviation string for <i>this</i> rank
 666          */
 667         public String getAbbreviation(){
 668                 if (this.equals(Rank.ORDER()) ){return "ordo";}
 669                 if (this.equals(Rank.FAMILY()) ){return "fam.";}
 670                 else if (this.equals(Rank.SUBFAMILY()) ){return "subfam.";}
 671                 else if (this.equals(Rank.TRIBE()) ){return "trib.";}
 672                 else if (this.equals(Rank.SUBTRIBE()) ){return "subtrib.";}
 673                 else if (this.equals(Rank.GENUS()) ){return "gen.";}
 674                 else if (this.equals(Rank.SUBGENUS()) ){return "subg.";}
 675                 else if (this.equals(Rank.SECTION()) ){return "sect.";}
 676                 else if (this.equals(Rank.SUBSECTION()) ){return "subsect.";}
 677                 else if (this.equals(Rank.SERIES()) ){return "ser.";}
 678                 //else if (this.equals(Rank.AGGREGATE()) ){return "aggr.";}
 679                 else if (this.equals(Rank.SPECIES()) ){return "sp.";}
 680                 else if (this.equals(Rank.SUBSPECIES()) ){return "subsp.";}
 681                 else if (this.equals(Rank.VARIETY()) ){return "var.";}
 682                 else if (this.equals(Rank.CONVAR()) ){return "convar.";}
 683                 else if (this.equals(Rank.SUBVARIETY()) ){return "subvar.";}
 684                 else if (this.equals(Rank.FORM()) ){return "f.";}
 685                 else if (this.equals(Rank.SPECIALFORM()) ){return "f.spec.";}
 686                 else if (this.equals(Rank.INFRAGENERICTAXON()) ){return "t.infgen.";}
 687                 else if (this.equals(Rank.INFRASPECIFICTAXON()) ){return "t.infr.";}
 688                 else {
 689                         logger.warn("Abbreviation for this Rank " + this.toString() +  " not yet implemented");
 690                         return "xxx.";
 691                 }
 692         }
 693
 694         @Override
 695         protected void setDefaultTerms(TermVocabulary<Rank> termVocabulary) {
 696                 Rank.BIOVARIETY = termVocabulary.findTermByUuid(Rank.uuidBioVariety);
 697                 Rank.CANDIDATE = termVocabulary.findTermByUuid(Rank.uuidCandidate);
 698                 Rank.CLASS = termVocabulary.findTermByUuid(Rank.uuidClass);
 699                 Rank.CONVAR = termVocabulary.findTermByUuid(Rank.uuidConvar);
 700                 Rank.CULTIVAR = termVocabulary.findTermByUuid(Rank.uuidCultivar);
 701                 Rank.CULTIVARGROUP = termVocabulary.findTermByUuid(Rank.uuidCultivarGroup);
 702                 Rank.DENOMINATIONCLASS = termVocabulary.findTermByUuid(Rank.uuidDenominationClass);
 703                 Rank.DIVISION = termVocabulary.findTermByUuid(Rank.uuidDivision);
 704                 Rank.DOMAIN = termVocabulary.findTermByUuid(Rank.uuidDomain);
 705                 Rank.EMPIRE = termVocabulary.findTermByUuid(Rank.uuidEmpire);
 706                 Rank.FAMILY = termVocabulary.findTermByUuid(Rank.uuidFamily);
 707                 Rank.FORM = termVocabulary.findTermByUuid(Rank.uuidForm);
 708                 Rank.GENUS = termVocabulary.findTermByUuid(Rank.uuidGenus);
 709                 Rank.GRAFTCHIMAERA = termVocabulary.findTermByUuid(Rank.uuidGraftChimaera);
 710                 Rank.GREX = termVocabulary.findTermByUuid(Rank.uuidGrex);
 711                 Rank.INFRACLASS = termVocabulary.findTermByUuid(Rank.uuidInfraclass);
 712                 Rank.INFRADIVISION = termVocabulary.findTermByUuid(Rank.uuidInfradivision);
 713                 Rank.INFRAFAMILY = termVocabulary.findTermByUuid(Rank.uuidInfrafamily);
 714                 Rank.INFRAGENERICTAXON = termVocabulary.findTermByUuid(Rank.uuidInfragenericTaxon);
 715                 Rank.INFRAGENUS = termVocabulary.findTermByUuid(Rank.uuidInfragenus);
 716                 Rank.INFRAKINGDOM = termVocabulary.findTermByUuid(Rank.uuidInfrakingdom);
 717                 Rank.INFRAORDER = termVocabulary.findTermByUuid(Rank.uuidInfraorder);
 718                 Rank.INFRAPHYLUM = termVocabulary.findTermByUuid(Rank.uuidInfraphylum);
 719                 Rank.INFRASPECIES = termVocabulary.findTermByUuid(Rank.uuidInfraspecies);
 720                 Rank.INFRASPECIFICTAXON = termVocabulary.findTermByUuid(Rank.uuidInfraspecificTaxon);
 721                 Rank.INFRATRIBE = termVocabulary.findTermByUuid(Rank.uuidInfratribe);
 722                 Rank.KINGDOM = termVocabulary.findTermByUuid(Rank.uuidKingdom);
 723                 Rank.ORDER = termVocabulary.findTermByUuid(Rank.uuidOrder);
 724                 Rank.PATHOVARIETY = termVocabulary.findTermByUuid(Rank.uuidPathoVariety);
 725                 Rank.PHYLUM = termVocabulary.findTermByUuid(Rank.uuidPhylum);
 726                 Rank.SECTION = termVocabulary.findTermByUuid(Rank.uuidSection);
 727                 Rank.SERIES = termVocabulary.findTermByUuid(Rank.uuidSeries);
 728                 Rank.SPECIALFORM = termVocabulary.findTermByUuid(Rank.uuidSpecialForm);
 729                 Rank.SPECIES = termVocabulary.findTermByUuid(Rank.uuidSpecies);
 730                 Rank.SPECIESAGGREGATE = termVocabulary.findTermByUuid(Rank.uuidSpeciesAggregate);
 731                 Rank.SUBCLASS = termVocabulary.findTermByUuid(Rank.uuidSubclass);
 732                 Rank.SUBDIVISION = termVocabulary.findTermByUuid(Rank.uuidSubdivision);
 733                 Rank.SUBFAMILY = termVocabulary.findTermByUuid(Rank.uuidSubfamily);
 734                 Rank.SUBFORM = termVocabulary.findTermByUuid(Rank.uuidSubform);
 735                 Rank.SUBGENUS = termVocabulary.findTermByUuid(Rank.uuidSubgenus);
 736                 Rank.SUBKINGDOM = termVocabulary.findTermByUuid(Rank.uuidSubkingdom);
 737                 Rank.SUBORDER = termVocabulary.findTermByUuid(Rank.uuidSuborder);
 738                 Rank.SUBPHYLUM = termVocabulary.findTermByUuid(Rank.uuidSubphylum);
 739                 Rank.SUBSECTION = termVocabulary.findTermByUuid(Rank.uuidSubsection);
 740                 Rank.SUBSERIES = termVocabulary.findTermByUuid(Rank.uuidSubseries);
 741                 Rank.SUBSPECIES = termVocabulary.findTermByUuid(Rank.uuidSubspecies);
 742                 Rank.SUBSPECIFICAGGREGATE = termVocabulary.findTermByUuid(Rank.uuidSubspecificAggregate);
 743                 Rank.SUBSUBFORM = termVocabulary.findTermByUuid(Rank.uuidSubsubform);
 744                 Rank.SUBSUBVARIETY = termVocabulary.findTermByUuid(Rank.uuidSubsubvariety);
 745                 Rank.SUBTRIBE = termVocabulary.findTermByUuid(Rank.uuidSubtribe);
 746                 Rank.SUBVARIETY = termVocabulary.findTermByUuid(Rank.uuidSubvariety);
 747                 Rank.SUPERCLASS = termVocabulary.findTermByUuid(Rank.uuidSuperclass);
 748                 Rank.SUPERDIVISION = termVocabulary.findTermByUuid(Rank.uuidSuperdivision);
 749                 Rank.SUPERFAMILY = termVocabulary.findTermByUuid(Rank.uuidSuperfamily);
 750                 Rank.SUPERKINGDOM = termVocabulary.findTermByUuid(Rank.uuidSuperkingdom);
 751                 Rank.SUPERORDER = termVocabulary.findTermByUuid(Rank.uuidSuperorder);
 752                 Rank.SUPERPHYLUM = termVocabulary.findTermByUuid(Rank.uuidSuperphylum);
 753                 Rank.SUPERTRIBE = termVocabulary.findTermByUuid(Rank.uuidSupertribe);
 754                 Rank.SUPRAGENERICTAXON = termVocabulary.findTermByUuid(Rank.uuidSupragenericTaxon);
 755                 Rank.TRIBE = termVocabulary.findTermByUuid(Rank.uuidTribe);
 756                 Rank.UNKNOWN_RANK = termVocabulary.findTermByUuid(Rank.uuidUnknownRank);
 757                 Rank.VARIETY = termVocabulary.findTermByUuid(Rank.uuidVariety);
 758         }
 759 }