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 java.util.HashMap;
  13 import java.util.List;
  14 import java.util.Map;
  15 import java.util.UUID;
  16
  17 import javax.persistence.Entity;
  18 import javax.persistence.Transient;
  19 import javax.xml.bind.annotation.XmlAccessType;
  20 import javax.xml.bind.annotation.XmlAccessorType;
  21 import javax.xml.bind.annotation.XmlType;
  22
  23 import org.apache.log4j.Logger;
  24 import org.hibernate.envers.Audited;
  25 import org.hibernate.search.annotations.Indexed;
  26
  27 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  28 import eu.etaxonomy.cdm.model.common.Language;
  29 import eu.etaxonomy.cdm.model.common.OrderedTermBase;
  30 import eu.etaxonomy.cdm.model.common.Representation;
  31 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  32 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  33
  34 /**
  35  * The class representing the taxonomical ranks (like "Family", "Genus" or
  36  * "Species") used for {@link TaxonNameBase taxon names} across all {@link NomenclaturalCode nomenclatural codes}
  37  * for bacteria (ICNB), viruses (ICVCN), plants and fungi (ICBN),
  38  * cultivars (ICNCP) and animals (ICZN).
  39  * <P>
  40  * A standard (ordered) list of taxonomical rank instances will be automatically
  41  * created as the project starts. But this class allows to extend this standard
  42  * list by creating new instances of additional taxonomical ranks if needed.
  43  * <P>
  44  * This class corresponds to: <ul>
  45  * <li> TaxonRankTerm according to the TDWG ontology
  46  * <li> TaxonomicRankEnum according to the TCS
  47  * <li> Rank according to the ABCD schema
  48  * </ul>
  49  *
  50  * @author m.doering
  51  * @version 1.0
  52  * @created 08-Nov-2007 13:06:46
  53  */
  54 @XmlAccessorType(XmlAccessType.FIELD)
  55 @XmlType(name = "Rank")
  56 @Entity
  57 @Indexed(index = "eu.etaxonomy.cdm.model.common.DefinedTermBase")
  58 @Audited
  59 public class Rank extends OrderedTermBase<Rank> {
  60         private static final long serialVersionUID = -8648081681348758485L;
  61         private static final Logger logger = Logger.getLogger(Rank.class);
  62
  63         private static final UUID uuidEmpire = UUID.fromString("ac470211-1586-4b24-95ca-1038050b618d");
  64         private static final UUID uuidDomain = UUID.fromString("ffca6ec8-8b88-417b-a6a0-f7c992aac19b");
  65         private static final UUID uuidSuperkingdom = UUID.fromString("64223610-7625-4cfd-83ad-b797bf7f0edd");
  66         private static final UUID uuidKingdom = UUID.fromString("fbe7109d-66b3-498c-a697-c6c49c686162");
  67         private static final UUID uuidSubkingdom = UUID.fromString("a71bd9d8-f3ab-4083-afb5-d89315d71655");
  68         private static final UUID uuidInfrakingdom = UUID.fromString("1e37930c-86cf-44f6-90fd-7822928df260");
  69         private static final UUID uuidSuperphylum = UUID.fromString("0d0cecb1-e254-4607-b210-6801e7ecbb04");
  70         private static final UUID uuidPhylum = UUID.fromString("773430d2-76b4-438c-b817-97a543a33287");
  71         private static final UUID uuidSubphylum = UUID.fromString("23a9b6ff-9408-49c9-bd9e-7a2ca5ab4725");
  72         private static final UUID uuidInfraphylum = UUID.fromString("1701de3a-7693-42a5-a2d3-42697f944190");
  73         private static final UUID uuidSuperdivision = UUID.fromString("a735a48f-4fc8-49a7-ae0c-6a984f658131");
  74         private static final UUID uuidDivision = UUID.fromString("7e56f5cc-123a-4fd1-8cbb-6fd80358b581");
  75         private static final UUID uuidSubdivision = UUID.fromString("931c840f-7a6b-4d76-ad38-bfdd77d7b2e8");
  76         private static final UUID uuidInfradivision = UUID.fromString("c0ede273-be52-4dee-b411-66ee08d30c94");
  77         private static final UUID uuidSuperclass = UUID.fromString("e65b4e1a-21ec-428d-9b9f-e87721ab967c");
  78         private static final UUID uuidClass = UUID.fromString("f23d14c4-1d34-4ee6-8b4e-eee2eb9a3daf");
  79         private static final UUID uuidSubclass = UUID.fromString("8cb26733-e2f5-46cb-ab5c-f99254f877aa");
  80         private static final UUID uuidInfraclass = UUID.fromString("ad23cfda-879a-4021-8629-c54d27caf717");
  81         private static final UUID uuidSuperorder = UUID.fromString("c8c67a22-301a-4219-b882-4a49121232ff");
  82         private static final UUID uuidOrder = UUID.fromString("b0785a65-c1c1-4eb4-88c7-dbd3df5aaad1");
  83         private static final UUID uuidSuborder = UUID.fromString("768ad378-fa85-42ab-b668-763225832f57");
  84         private static final UUID uuidInfraorder = UUID.fromString("84099182-a6f5-47d7-8586-33c9e9955a10");
  85         private static final UUID uuidSectionZoology = UUID.fromString("691d371e-10d7-43f0-93db-3d7fa1a62c54");
  86         private static final UUID uuidSubsectionZoology = UUID.fromString("0ed32d28-adc4-4303-a9ca-68e2acd67e33");
  87         private static final UUID uuidSuperfamily = UUID.fromString("2cfa510a-dcea-4a03-b66a-b1528f9b0796");
  88         private static final UUID uuidFamily = UUID.fromString("af5f2481-3192-403f-ae65-7c957a0f02b6");
  89         private static final UUID uuidSubfamily = UUID.fromString("862526ee-7592-4760-a23a-4ff3641541c5");
  90         private static final UUID uuidInfrafamily = UUID.fromString("c3f2e3bb-6eef-4a26-9fb7-b14f4c8c5e4f");
  91         private static final UUID uuidSupertribe = UUID.fromString("11e94828-8c61-499b-87d6-1de35ce2c51c");
  92         private static final UUID uuidTribe = UUID.fromString("4aa6890b-0363-4899-8d7c-ee0cb78e6166");
  93         private static final UUID uuidSubtribe = UUID.fromString("ae41ecc5-5165-4126-9d24-79939ae5d822");
  94         private static final UUID uuidInfratribe = UUID.fromString("1ec02e8f-f2b7-4c65-af9f-b436b34c79a3");
  95         private static final UUID uuidSupragenericTaxon = UUID.fromString("1fdc0b93-c354-441a-8406-091e0303ff5c");
  96         private static final UUID uuidGenus = UUID.fromString("1b11c34c-48a8-4efa-98d5-84f7f66ef43a");
  97         private static final UUID uuidSubgenus = UUID.fromString("78786e16-2a70-48af-a608-494023b91904");
  98         private static final UUID uuidInfragenus = UUID.fromString("a9972969-82cd-4d54-b693-a096422f13fa");
  99         private static final UUID uuidSectionBotany = UUID.fromString("3edff68f-8527-49b5-bf91-7e4398bb975c");
 100         private static final UUID uuidSubsectionBotany = UUID.fromString("d20f5b61-d463-4448-8f8a-c1ff1f262f59");
 101         private static final UUID uuidSeries = UUID.fromString("d7381ecf-48f8-429b-9c54-f461656978cd");
 102         private static final UUID uuidSubseries = UUID.fromString("80c9a263-f4db-4a13-b6c2-b7fec1aa1200");
 103         private static final UUID uuidSpeciesAggregate = UUID.fromString("1ecae058-4217-4f75-9c27-6d8ba099ac7a");
 104         private static final UUID uuidSpeciesGroup = UUID.fromString("d1988a11-292b-46fa-8fb7-bc64ea6d8fc6");
 105         private static final UUID uuidInfragenericTaxon = UUID.fromString("41bcc6ac-37d3-4fd4-bb80-3cc5b04298b9");
 106         public static final UUID uuidSpecies = UUID.fromString("b301f787-f319-4ccc-a10f-b4ed3b99a86d");
 107         private static final UUID uuidSubspecificAggregate = UUID.fromString("72c248b9-027d-4402-b375-dd4f0850c9ad");
 108         private static final UUID uuidSubspecies = UUID.fromString("462a7819-8b00-4190-8313-88b5be81fad5");
 109         private static final UUID uuidInfraspecies = UUID.fromString("f28ebc9e-bd50-4194-9af1-42f5cb971a2c");
 110         private static final UUID uuidNatio = UUID.fromString("965f2f38-7f97-4270-ab5a-1999bf050a22");
 111         private static final UUID uuidVariety = UUID.fromString("d5feb6a5-af5c-45ef-9878-bb4f36aaf490");
 112         private static final UUID uuidBioVariety = UUID.fromString("a3a364cb-1a92-43fc-a717-3c44980a0991");
 113         private static final UUID uuidPathoVariety = UUID.fromString("2f4f4303-a099-47e3-9048-d749d735423b");
 114         private static final UUID uuidSubvariety = UUID.fromString("9a83862a-7aee-480c-a98d-4bceaf8712ca");
 115         private static final UUID uuidSubsubvariety = UUID.fromString("bff22f84-553a-4429-a4e7-c4b3796c3a18");
 116         private static final UUID uuidConvar = UUID.fromString("2cc740c9-cebb-43c8-9b06-1bef79e6a56a");
 117         private static final UUID uuidForm = UUID.fromString("0461281e-458a-47b9-8d41-19a3d39356d5");
 118         private static final UUID uuidSpecialForm = UUID.fromString("bed20aee-2f5a-4635-9c02-eff06246d067");
 119         private static final UUID uuidSubform = UUID.fromString("47cfc5b0-0fb7-4ceb-b61d-e1dd8de8b569");
 120         private static final UUID uuidSubsubform = UUID.fromString("1c8ac389-4349-4ae0-87be-7239f6635068");
 121         private static final UUID uuidInfraspecificTaxon = UUID.fromString("eb75c27d-e154-4570-9d96-227b2df60474");
 122         private static final UUID uuidCandidate = UUID.fromString("ead9a1f5-dfd4-4de2-9121-70a47accb10b");
 123         private static final UUID uuidDenominationClass = UUID.fromString("49bdf74a-2170-40ed-8be2-887a0db517bf");
 124         private static final UUID uuidGrex = UUID.fromString("08dcb4ff-ac58-48a3-93af-efb3d836ac84");
 125         private static final UUID uuidGraftChimaera = UUID.fromString("6b4063bc-f934-4796-9bf3-0ef3aea5c1cb");
 126         private static final UUID uuidCultivarGroup = UUID.fromString("d763e7d3-e7de-4bb1-9d75-225ca6948659");
 127         private static final UUID uuidCultivar = UUID.fromString("5e98415b-dc6e-440b-95d6-ea33dbb39ad0");
 128         private static final UUID uuidUnknownRank = UUID.fromString("5c4d6755-2cf6-44ca-9220-cccf8881700b");
 129 //      private static final UUID uuidUnrankedInfraSpecific = UUID.fromString("a965befb-70a9-4747-a18f-624456c65223");
 130 //      private static final UUID uuidUnrankedInfraGeneric = UUID.fromString("994646a1-c2e7-461d-a1bc-2afd6ea51b40");
 131
 132         private static Map<String, UUID> abbrevMap = null;
 133         private static Map<String, UUID> labelMap = null;
 134
 135         protected static Map<UUID, Rank> termMap = null;
 136
 137
 138 // ********************* CONSTRUCTORS ************************************+/
 139         /**
 140          * Class constructor: creates a new empty rank instance.
 141          *
 142          * @see         #Rank(String, String, String)
 143          */
 144         public Rank() {
 145         }
 146
 147         /**
 148          * Class constructor: creates an additional rank instance with a description
 149          * (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label and a label abbreviation.
 150          *
 151          * @param       term             the string (in the default language) describing the
 152          *                                               new rank to be created
 153          * @param       label            the string identifying the new rank to be created
 154          * @param       labelAbbrev  the string identifying (in abbreviated form) the
 155          *                                               new rank to be created
 156          * @see         #Rank()
 157          */
 158         public Rank(String term, String label, String labelAbbrev) {
 159                 super(term, label, labelAbbrev);
 160         }
 161
 162         /**
 163          * Creates a new empty rank.
 164          *
 165          * @see #NewInstance(String, String, String)
 166          */
 167         private static Rank NewInstance(){
 168                 return new Rank();
 169         }
 170
 171         /**
 172          * Creates an additional rank with a description (in the {@link Language#DEFAULT() default language}),
 173          * a label and a label abbreviation.
 174          *
 175          * @param       term             the string (in the default language) describing the
 176          *                                               new rank to be created
 177          * @param       label            the string identifying the new rank to be created
 178          * @param       labelAbbrev  the string identifying (in abbreviated form) the
 179          *                                               new rank to be created
 180          * @see                                  #NewInstance()
 181          */
 182         private static Rank NewInstance(String term, String label, String labelAbbrev){
 183                 return new Rank(term, label, labelAbbrev);
 184         }
 185
 186 //********* METHODS **************************************/
 187
 188         /* (non-Javadoc)
 189          * @see eu.etaxonomy.cdm.model.common.DefinedTermBase#resetTerms()
 190          */
 191         @Override
 192         public void resetTerms(){
 193                 termMap = null;
 194         }
 195
 196
 197
 198         protected static Rank getTermByUuid(UUID uuid){
 199                 if (termMap == null){
 200                         return null;  //better return null then initialize the termMap in an unwanted way
 201                 }
 202                 return (Rank)termMap.get(uuid);
 203         }
 204
 205         public static final Rank EMPIRE(){
 206           return getTermByUuid(uuidEmpire);
 207         }
 208         public static final Rank DOMAIN(){
 209                   return getTermByUuid(uuidDomain);
 210         }
 211         public static final Rank SUPERKINGDOM(){
 212                 return getTermByUuid(uuidSuperkingdom);
 213         }
 214         public static final Rank KINGDOM(){
 215                 return getTermByUuid(uuidKingdom);
 216         }
 217         public static final Rank SUBKINGDOM(){
 218                 return getTermByUuid(uuidSubkingdom);
 219         }
 220         public static final Rank INFRAKINGDOM(){
 221                 return getTermByUuid(uuidInfrakingdom);
 222         }
 223         public static final Rank SUPERPHYLUM(){
 224                 return getTermByUuid(uuidSuperphylum);
 225         }
 226         public static final Rank PHYLUM(){
 227                 return getTermByUuid(uuidPhylum);
 228         }
 229         public static final Rank SUBPHYLUM(){
 230                 return getTermByUuid(uuidSubphylum);
 231         }
 232         public static final Rank INFRAPHYLUM(){
 233                 return getTermByUuid(uuidInfraphylum);
 234         }
 235         public static final Rank SUPERDIVISION(){
 236                 return getTermByUuid(uuidSuperdivision);
 237         }
 238         public static final Rank DIVISION(){
 239                 return getTermByUuid(uuidDivision);
 240         }
 241         public static final Rank SUBDIVISION(){
 242                 return getTermByUuid(uuidSubdivision);
 243         }
 244         public static final Rank INFRADIVISION(){
 245                 return getTermByUuid(uuidInfradivision);
 246         }
 247         public static final Rank SUPERCLASS(){
 248                 return getTermByUuid(uuidSuperclass);
 249         }
 250         public static final Rank CLASS(){
 251                 return getTermByUuid(uuidClass);
 252         }
 253         public static final Rank SUBCLASS(){
 254                 return getTermByUuid(uuidSubclass);
 255         }
 256         public static final Rank INFRACLASS(){
 257                 return getTermByUuid(uuidInfraclass);
 258         }
 259         public static final Rank SUPERORDER(){
 260                 return getTermByUuid(uuidSuperorder);
 261         }
 262         public static final Rank ORDER(){
 263                 return getTermByUuid(uuidOrder);
 264         }
 265         public static final Rank SUBORDER(){
 266                 return getTermByUuid(uuidSuborder);
 267         }
 268         public static final Rank INFRAORDER(){
 269                 return getTermByUuid(uuidInfraorder);
 270         }
 271         public static final Rank SUPERFAMILY(){
 272                 return getTermByUuid(uuidSuperfamily);
 273         }
 274         public static final Rank FAMILY(){
 275                 return getTermByUuid(uuidFamily);
 276         }
 277         public static final Rank SUBFAMILY(){
 278                 return getTermByUuid(uuidSubfamily);
 279         }
 280         public static final Rank INFRAFAMILY(){
 281                 return getTermByUuid(uuidInfrafamily);
 282         }
 283         public static final Rank SUPERTRIBE(){
 284                 return getTermByUuid(uuidSupertribe);
 285         }
 286         public static final Rank TRIBE(){
 287                 return getTermByUuid(uuidTribe);
 288         }
 289         public static final Rank SUBTRIBE(){
 290                 return getTermByUuid(uuidSubtribe);
 291         }
 292         public static final Rank INFRATRIBE(){
 293                 return getTermByUuid(uuidInfratribe);
 294         }
 295         public static final Rank SUPRAGENERICTAXON(){
 296                 return getTermByUuid(uuidSupragenericTaxon);
 297         }
 298         public static final Rank GENUS(){
 299                 return getTermByUuid(uuidGenus);
 300         }
 301         public static final Rank SUBGENUS(){
 302                 return getTermByUuid(uuidSubgenus);
 303         }
 304         public static final Rank INFRAGENUS(){
 305                 return getTermByUuid(uuidInfragenus);
 306         }
 307         public static final Rank SECTION_BOTANY(){
 308                 return getTermByUuid(uuidSectionBotany);
 309         }
 310         public static final Rank SUBSECTION_BOTANY(){
 311                 return getTermByUuid(uuidSubsectionBotany);
 312         }
 313         public static final Rank SECTION_ZOOLOGY(){
 314                 return getTermByUuid(uuidSectionZoology);
 315         }
 316         public static final Rank SUBSECTION_ZOOLOGY(){
 317                 return getTermByUuid(uuidSubsectionZoology);
 318         }
 319         public static final Rank SERIES(){
 320                 return getTermByUuid(uuidSeries);
 321         }
 322         public static final Rank SUBSERIES(){
 323                 return getTermByUuid(uuidSubseries);
 324         }
 325         public static final Rank SPECIESAGGREGATE(){
 326                 return getTermByUuid(uuidSpeciesAggregate);
 327         }
 328         public static final Rank SPECIESGROUP(){
 329                 return getTermByUuid(uuidSpeciesGroup);
 330         }
 331         /**
 332          * 'Unranked infrageneric'. An infrageneric rank which is on purpose not further defined.
 333          * This sometimes holds for names from the 19th century.
 334          */
 335
 336         public static final Rank INFRAGENERICTAXON(){
 337                 return getTermByUuid(uuidInfragenericTaxon);
 338         }
 339         public static final Rank SPECIES(){
 340                 return getTermByUuid(uuidSpecies);
 341         }
 342         public static final Rank SUBSPECIFICAGGREGATE(){
 343                 return getTermByUuid(uuidSubspecificAggregate);
 344         }
 345         public static final Rank SUBSPECIES(){
 346                 return getTermByUuid(uuidSubspecies);
 347         }
 348         public static final Rank INFRASPECIES(){
 349                 return getTermByUuid(uuidInfraspecies);
 350         }
 351         public static final Rank VARIETY(){
 352                 return getTermByUuid(uuidVariety);
 353         }
 354         public static final Rank BIOVARIETY(){
 355                 return getTermByUuid(uuidBioVariety);
 356         }
 357         public static final Rank PATHOVARIETY(){
 358                 return getTermByUuid(uuidPathoVariety);
 359         }
 360         public static final Rank SUBVARIETY(){
 361                 return getTermByUuid(uuidSubvariety);
 362         }
 363         public static final Rank SUBSUBVARIETY(){
 364                 return getTermByUuid(uuidSubsubvariety );
 365         }
 366         public static final Rank CONVAR(){
 367                 return getTermByUuid(uuidConvar);
 368         }
 369         public static final Rank FORM(){
 370                 return getTermByUuid(uuidForm);
 371         }
 372         public static final Rank SPECIALFORM(){
 373                 return getTermByUuid(uuidSpecialForm);
 374         }
 375         public static final Rank SUBFORM(){
 376                 return getTermByUuid(uuidSubform);
 377         }
 378         public static final Rank SUBSUBFORM(){
 379                 return getTermByUuid(uuidSubsubform);
 380         }
 381         /**
 382          * 'Unranked infraspecific'. An infraspecific rank which is on purpose not further defined.
 383          * This sometimes holds for names from the 19th century.
 384          */
 385         public static final Rank INFRASPECIFICTAXON(){
 386                 return getTermByUuid(uuidInfraspecificTaxon);
 387         }
 388         public static final Rank CANDIDATE(){
 389                 return getTermByUuid(uuidCandidate);
 390         }
 391         public static final Rank DENOMINATIONCLASS(){
 392                 return getTermByUuid(uuidDenominationClass);
 393         }
 394         public static final Rank GREX(){
 395                 return getTermByUuid(uuidGrex);
 396         }
 397         public static final Rank GRAFTCHIMAERA(){
 398                 return getTermByUuid(uuidGraftChimaera);
 399         }
 400         public static final Rank CULTIVARGROUP(){
 401                 return getTermByUuid(uuidCultivarGroup);
 402         }
 403         public static final Rank CULTIVAR(){
 404                 return getTermByUuid(uuidCultivar);
 405         }
 406         public static final Rank UNKNOWN_RANK(){
 407                 return getTermByUuid(uuidUnknownRank);
 408         }
 409         public static final Rank NATIO(){
 410                 return getTermByUuid(uuidNatio);
 411         }
 412         /**
 413          * @see #INFRASPECIFICTAXON()
 414          */
 415         public static final Rank UNRANKED_INFRASPECIFIC(){
 416                 return getTermByUuid(uuidInfraspecificTaxon);
 417         }
 418         /**
 419          * @see #INFRAGENERICTAXON()
 420          */
 421         public static final Rank UNRANKED_INFRAGENERIC(){
 422                 return getTermByUuid(uuidInfragenericTaxon);
 423         }
 424
 425         /**
 426          * Returns the boolean value indicating whether <i>this</i> rank is higher than
 427          * the genus rank (true) or not (false). Returns false if <i>this</i> rank is null.
 428          *
 429          * @see  #isGenus()
 430          * @see  #isInfraGeneric()
 431          * @see  #isSpecies()
 432          * @see  #isInfraSpecific()
 433          */
 434         @Transient
 435         public boolean isSupraGeneric(){
 436                 return (this.isHigher(Rank.GENUS()));
 437         }
 438
 439         /**
 440          * Returns the boolean value indicating whether <i>this</i> rank is the genus rank
 441          * (true) or not (false). Returns false if <i>this</i> rank is null.
 442          *
 443          * @see  #isSupraGeneric()
 444          * @see  #isInfraGeneric()
 445          * @see  #isSpecies()
 446          * @see  #isInfraSpecific()
 447          */
 448         @Transient
 449         public boolean isGenus(){
 450                 return (this.equals(Rank.GENUS()));
 451         }
 452
 453         /**
 454          * Returns the boolean value indicating whether <i>this</i> rank is higher than the
 455          * species rank and lower than the genus rank (true) or not (false). Species groups or
 456          * aggregates are also handled as infrageneric ranks.
 457          * Returns false if <i>this</i> rank is null.
 458          *
 459          * @see  #isSupraGeneric()
 460          * @see  #isGenus()
 461          * @see  #isSpeciesAggregate()
 462          * @see  #isSpecies()
 463          * @see  #isInfraSpecific()
 464          */
 465         @Transient
 466         public boolean isInfraGeneric(){
 467                 return (this.isLower(Rank.GENUS()) && this.isHigher(Rank.SPECIES()));
 468         }
 469
 470         /**
 471          * Returns true if this rank indicates a rank that aggregates species
 472          * like species aggregates or species groups, false otherwise. This methods
 473          * currently returns false for all user defined ranks.
 474          * @return
 475          */
 476         @Transient
 477         public boolean isSpeciesAggregate(){
 478                 return (this.equals(Rank.SPECIESAGGREGATE()) || (this.isLower(Rank.SPECIESAGGREGATE()) && this.isHigher(Rank.SPECIES())));
 479         }
 480
 481         /**
 482          * Returns the boolean value indicating whether <i>this</i> rank is the species
 483          * rank (true) or not (false). Returns false if <i>this</i> rank is null.
 484          *
 485          * @see  #isSupraGeneric()
 486          * @see  #isGenus()
 487          * @see  #isInfraGeneric()
 488          * @see  #isInfraSpecific()
 489          */
 490         @Transient
 491         public boolean isSpecies(){
 492                 return (this.equals(Rank.SPECIES()));
 493         }
 494
 495         /**
 496          * Returns the boolean value indicating whether <i>this</i> rank is lower than the
 497          * species rank (true) or not (false). Returns false if <i>this</i> rank is null.
 498          *
 499          * @see  #isSupraGeneric()
 500          * @see  #isGenus()
 501          * @see  #isInfraGeneric()
 502          * @see  #isSpecies()
 503          */
 504         @Transient
 505         public boolean isInfraSpecific(){
 506                 return (this.isLower(Rank.SPECIES()));
 507         }
 508
 509
 510         /**
 511          * Returns the rank identified through a name (abbreviated or not).
 512          * Preliminary implementation for BotanicalNameParser.
 513          *
 514          * @param       strRank the string identifying the rank
 515          * @return              the rank
 516          */
 517         public static Rank getRankByNameOrAbbreviation(String strRank)
 518                                 throws UnknownCdmTypeException{
 519                 return getRankByNameOrAbbreviation(strRank, false);
 520         }
 521
 522         /**
 523          * Returns the rank identified through a name (abbreviated or not) for a given nomenclatural code.
 524          * Preliminary implementation for BotanicalNameParser.
 525          *
 526          * @param       strRank the string identifying the rank
 527          * @param   nc      the nomenclatural code
 528          * @return              the rank
 529          */
 530         public static Rank getRankByNameOrAbbreviation(String strRank, NomenclaturalCode nc)
 531                                 throws UnknownCdmTypeException{
 532                 return getRankByNameOrAbbreviation(strRank, nc, false);
 533         }
 534
 535         // TODO
 536         // Preliminary implementation for BotanicalNameParser.
 537         // not yet complete
 538         /**
 539          * Returns the rank identified through a name (abbreviated or not).
 540          * Preliminary implementation for BotanicalNameParser.
 541          *
 542          * @param       strRank the string identifying the rank
 543          * @param       useUnknown      if true the rank UNKNOWN_RANK is returned if the abbrev is
 544          *                      unknown or not yet implemented
 545          * @return              the rank
 546          */
 547         public static Rank getRankByNameOrAbbreviation(String strRank, boolean useUnknown)
 548                         throws UnknownCdmTypeException{
 549                 try {
 550                         return getRankByAbbreviation(strRank);
 551                 } catch (UnknownCdmTypeException e) {
 552                         return getRankByName(strRank, useUnknown);
 553                 }
 554         }
 555
 556         // TODO
 557         // Preliminary implementation for BotanicalNameParser.
 558         // not yet complete
 559         /**
 560          * Returns the rank identified through a name (abbreviated or not).
 561          * Preliminary implementation for BotanicalNameParser.
 562          *
 563          * @param       strRank the string identifying the rank
 564          * @param   nc      the nomenclatural code
 565          * @param       useUnknown      if true the rank UNKNOWN_RANK is returned if the abbrev is
 566          *                      unknown or not yet implemented
 567          * @return              the rank
 568          */
 569         public static Rank getRankByNameOrAbbreviation(String strRank, NomenclaturalCode nc, boolean useUnknown)
 570                         throws UnknownCdmTypeException{
 571                 try {
 572                         return getRankByAbbreviation(strRank, nc);
 573                 } catch (UnknownCdmTypeException e) {
 574                         return getRankByName(strRank, nc, useUnknown);
 575                 }
 576         }
 577
 578         /**
 579          * Returns the rank identified through an abbreviated name.
 580          * Preliminary implementation for BotanicalNameParser.<BR>
 581          * Note: For abbrev = "[unranked]" the result is undefined.
 582          * It maybe the infrageneric unranked or the infraspecific unranked.
 583          * You need to define by context which one is correct.
 584          *
 585          * @param       abbrev  the string for the name abbreviation
 586          * @return              the rank
 587          */
 588         public static Rank getRankByAbbreviation(String abbrev)
 589                                                 throws UnknownCdmTypeException{
 590                 return getRankByAbbreviation(abbrev, false);
 591         }
 592
 593         /**
 594          * Returns the rank identified through an abbreviated name for a given nomenclatural code.
 595          * See also {@link #getRankByAbbreviation(String, boolean)}
 596          *
 597          * @param       abbrev  the string for the name abbreviation
 598          * @param       nc          the nomenclatural code
 599          * @return              the rank
 600          */
 601         public static Rank getRankByAbbreviation(String abbrev, NomenclaturalCode nc) throws UnknownCdmTypeException{
 602                 return getRankByAbbreviation(abbrev, nc, false);
 603         }
 604
 605         // TODO
 606         // Preliminary implementation for BotanicalNameParser.
 607         // not yet complete
 608         /**
 609          * Returns the rank identified through an abbreviated representation.
 610          * At the moment it uses the English abbreviations (being Latin because
 611          * we do not have Latin representations yet.
 612          * TODO
 613          * If no according abbreviation is available it throws either an UnknownCdmTypeException
 614          * or an #Rank.UNKNOWN() object depending on the useUnknown flag.
 615          *
 616          * @param       abbrev          the string for the name abbreviation
 617          * @param       useUnknown      if true the rank UNKNOWN_RANK is returned if the abbrev is
 618          *                      unknown or not yet existent
 619          * @return  the rank
 620          */
 621         public static Rank getRankByAbbreviation(String abbrev, boolean useUnknown) throws UnknownCdmTypeException{
 622                 Rank result = null;
 623                 if (abbrev == null){
 624                         throw new NullPointerException("Abbrev is NULL in getRankByAbbreviation");
 625                 }
 626                 if (abbrev.trim().equals("")){
 627                         //handle empty abbrev as unknown
 628                         abbrev = "oijaämöö";
 629                 }
 630                 if (abbrevMap == null){
 631                         return null;
 632                 }
 633                 UUID uuid = abbrevMap.get(abbrev);
 634                 if (uuid != null ){
 635                         result = getTermByUuid(uuid);
 636                 }
 637                 if (result != null){
 638                         return result;
 639                 }else {
 640                         if (abbrev == null){
 641                                 abbrev = "(null)";
 642                         }
 643                         if (useUnknown){
 644                                 logger.info("Unknown rank name: " + abbrev + ". Rank 'UNKNOWN_RANK' created instead");
 645                                 return Rank.UNKNOWN_RANK();
 646                         }else{
 647                                 throw new UnknownCdmTypeException("Unknown rank abbreviation: " + abbrev);
 648                         }
 649                 }
 650         }
 651
 652         // TODO
 653         // Preliminary implementation to cover Botany and Zoology.
 654         /**
 655          * Returns the rank identified through an abbreviated name for a given nomenclatural code.
 656          * Preliminary implementation for ICBN and ICZN.
 657          * See also {@link #getRankByAbbreviation(String, boolean)}
 658
 659          *
 660          * @param       abbrev          the string for the name abbreviation
 661          * @param       nc              the nomenclatural code
 662          * @param       useUnknown      if true the rank UNKNOWN_RANK is returned if the abbrev is
 663          *                      unknown or not yet implemented
 664          * @return  the rank
 665          */
 666         public static Rank getRankByAbbreviation(String abbrev, NomenclaturalCode nc,  boolean useUnknown)
 667                 throws UnknownCdmTypeException{
 668
 669                 if (nc != null && nc.equals(NomenclaturalCode.ICZN)) {
 670                         if (abbrev.equalsIgnoreCase("sect.")) { return Rank.SECTION_ZOOLOGY();
 671                         } else if (abbrev.equalsIgnoreCase("subsect.")) { return Rank.SUBSECTION_ZOOLOGY();
 672                         }
 673                 }
 674                 return getRankByAbbreviation(abbrev, useUnknown);
 675         }
 676
 677         // TODO
 678         // Preliminary implementation for BotanicalNameParser.
 679         // not yet complete
 680         /**
 681          * Returns the rank identified through a name.
 682          * Preliminary implementation for BotanicalNameParser.
 683          *
 684          * @param       rankName        the string for the name of the rank
 685          * @return                      the rank
 686          */
 687         public static Rank getRankByName(String rankName) throws UnknownCdmTypeException{
 688                 return getRankByName(rankName, false);
 689         }
 690
 691
 692         // TODO
 693         // Preliminary implementation for ICBN and ICZN.
 694         // not yet complete
 695         /**
 696          * Returns the rank identified through a name for a given nomenclatural code.
 697          * Preliminary implementation for ICBN and ICZN.
 698          *
 699          * @param       rankName        the string for the name of the rank
 700          * @param       nc              the nomenclatural code
 701          * @return                      the rank
 702          */
 703         public static Rank getRankByName(String rankName, NomenclaturalCode nc) throws UnknownCdmTypeException{
 704                 return getRankByName(rankName, nc, false);
 705         }
 706
 707         /**
 708          * Returns the rank identified through a name.
 709          * Preliminary implementation for BotanicalNameParser.
 710          * TODO At the moment we do not have Latin representations yet.
 711          *
 712          * @param       rankName        the string for the name of the rank
 713          * @param       useUnknown      if true the rank UNKNOWN_RANK is returned if the rank name is
 714          *                      unknown or not yet implemented
 715          * @return                      the rank
 716          */
 717         public static Rank getRankByName(String rankName, boolean useUnknown)
 718                         throws UnknownCdmTypeException{
 719                 if (rankName.equalsIgnoreCase("Regnum")){ return Rank.KINGDOM();
 720                 }else if (rankName.equalsIgnoreCase("Subregnum")){ return Rank.SUBKINGDOM();
 721                 }else if (rankName.equalsIgnoreCase("Phylum")){ return Rank.PHYLUM();
 722                 }else if (rankName.equalsIgnoreCase("Subphylum")){ return Rank.SUBPHYLUM();
 723                 }else if (rankName.equalsIgnoreCase("Divisio")){ return Rank.DIVISION();
 724                 }else if (rankName.equalsIgnoreCase("Subdivisio")){ return Rank.SUBDIVISION();
 725                 }else if (rankName.equalsIgnoreCase("Classis")){ return Rank.CLASS();
 726                 }else if (rankName.equalsIgnoreCase("Subclassis")){ return Rank.SUBCLASS();
 727                 }else if (rankName.equalsIgnoreCase("Superordo")){ return Rank.SUPERORDER();
 728                 }else if (rankName.equalsIgnoreCase("Ordo")){ return Rank.ORDER();
 729                 }else if (rankName.equalsIgnoreCase("Subordo")){ return Rank.SUBORDER();
 730                 }else if (rankName.equalsIgnoreCase("Familia")){ return Rank.FAMILY();
 731                 }else if (rankName.equalsIgnoreCase("Subfamilia")){ return Rank.SUBFAMILY();
 732                 }else if (rankName.equalsIgnoreCase("Tribus")){ return Rank.TRIBE();
 733                 }else if (rankName.equalsIgnoreCase("Subtribus")){ return Rank.SUBTRIBE();
 734                 }else if (rankName.equalsIgnoreCase("Genus")){ return Rank.GENUS();
 735                 }else if (rankName.equalsIgnoreCase("Subgenus")){ return Rank.SUBGENUS();
 736                 }else if (rankName.equalsIgnoreCase("Sectio")){ return Rank.SECTION_BOTANY();
 737                 }else if (rankName.equalsIgnoreCase("Subsectio")){ return Rank.SUBSECTION_BOTANY();
 738                 }else if (rankName.equalsIgnoreCase("Series")){ return Rank.SERIES();
 739                 }else if (rankName.equalsIgnoreCase("Subseries")){ return Rank.SUBSERIES();
 740                 }else if (rankName.equalsIgnoreCase("Aggregate")){ return Rank.SPECIESAGGREGATE();
 741                 }else if (rankName.equalsIgnoreCase("Speciesgroup")){ return Rank.SPECIESGROUP();
 742                 }else if (rankName.equalsIgnoreCase("Species")){ return Rank.SPECIES();
 743                 }else if (rankName.equalsIgnoreCase("Subspecies")){ return Rank.SUBSPECIES();
 744                 }else if (rankName.equalsIgnoreCase("Convarietas")){ return Rank.CONVAR();
 745                 }else if (rankName.equalsIgnoreCase("Varietas")){ return Rank.VARIETY();
 746                 }else if (rankName.equalsIgnoreCase("Subvarietas")){ return Rank.SUBVARIETY();
 747                 }else if (rankName.equalsIgnoreCase("Forma")){ return Rank.FORM();
 748                 }else if (rankName.equalsIgnoreCase("Subforma")){ return Rank.SUBFORM();
 749                 }else if (rankName.equalsIgnoreCase("Forma spec.")){ return Rank.SPECIALFORM();
 750                 }else if (rankName.equalsIgnoreCase("tax.infragen.")){ return Rank.INFRAGENERICTAXON();
 751                 }else if (rankName.equalsIgnoreCase("tax.infrasp.")){ return Rank.INFRASPECIFICTAXON();
 752                 // old ranks
 753                 }else if (rankName.equalsIgnoreCase("proles")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
 754                 }else if (rankName.equalsIgnoreCase("race")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
 755                 }else if (rankName.equalsIgnoreCase("taxon")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
 756                 }else if (rankName.equalsIgnoreCase("sublusus")){ return Rank.INFRASPECIFICTAXON(); //to create the name put prol. and the infraspeciesepi to the field unnamed namephrase
 757
 758                 }else{
 759                         if (rankName == null){
 760                                 rankName = "(null)";  //see NPE above
 761                         }
 762                         if (useUnknown){
 763                                 logger.info("Unknown rank name: " + rankName+". Rank 'UNKNOWN_RANK' created instead");
 764                                 return Rank.UNKNOWN_RANK();
 765                         }else{
 766                                 throw new UnknownCdmTypeException("Unknown rank name: " + rankName);
 767                         }
 768                 }
 769         }
 770
 771         /**
 772          * Defines the rank according to the English name.
 773          * @param rankName English rank name.
 774          * @param nc Defines the handling of the section and subsection ranks. These are in different orders depending on the
 775          * nomenclatural code.
 776          * @param useUnknown if true, the "Unknown" rank is returned as a placeholder.
 777          * @return
 778          * @throws UnknownCdmTypeException never thrown if useUnknown is true
 779          */
 780         public static Rank getRankByEnglishName(String rankName, NomenclaturalCode nc, boolean useUnknown) throws UnknownCdmTypeException{
 781                 Rank result = null;
 782                 if (rankName == null){
 783                         throw new NullPointerException("Abbrev is NULL in getRankByAbbreviation");
 784                 }
 785                 if (labelMap == null){
 786                         return null;
 787                 }
 788                 //handle section and subsection (not unique representations)
 789                 if (rankName.equalsIgnoreCase("Section")){
 790                         if (nc != null && nc.equals(NomenclaturalCode.ICZN)){   return Rank.SECTION_ZOOLOGY();
 791                         }else if (nc != null && nc.equals(NomenclaturalCode.ICBN)){return Rank.SECTION_BOTANY();
 792                         }else{
 793                                 String errorWarning = "Section is only defined for ICZN and ICBN at the moment but here needed for " + ((nc == null)? "(null)": nc.toString());
 794                                 logger.warn(errorWarning);
 795                                 throw new UnknownCdmTypeException (errorWarning);
 796                         }
 797                 }else if (rankName.equalsIgnoreCase("Subsection")){
 798                         if (nc != null && nc.equals(NomenclaturalCode.ICZN)){ return Rank.SECTION_ZOOLOGY();
 799                         }else if (nc != null && nc.equals(NomenclaturalCode.ICBN)){ return Rank.SECTION_BOTANY();
 800                         }else{
 801                                 String errorWarning = "Subsection is only defined for ICZN and ICBN at the moment but here needed for " + ((nc == null)? "(null)": nc.toString());
 802                                 logger.warn(errorWarning);
 803                                 throw new UnknownCdmTypeException (errorWarning);
 804                         }
 805                 }
 806
 807                 rankName = rankName.toLowerCase();
 808
 809                 UUID uuid = labelMap.get(rankName);
 810                 if (uuid != null ){
 811                         result = getTermByUuid(uuid);
 812                 }
 813                 if (result != null){
 814                         return result;
 815                 }else {
 816                         if (rankName == null){
 817                                 rankName = "(null)";
 818                         }
 819                         if (useUnknown){
 820                                 logger.info("Unknown rank name: " + rankName + ". Rank 'UNKNOWN_RANK' created instead");
 821                                 return Rank.UNKNOWN_RANK();
 822                         }else{
 823                                 throw new UnknownCdmTypeException("Unknown rank: " + rankName);
 824                         }
 825                 }
 826         }
 827
 828
 829         public static Rank getRankByName(String rankName, NomenclaturalCode nc, boolean useUnknown)
 830                 throws UnknownCdmTypeException {
 831
 832                 if (nc.equals(NomenclaturalCode.ICZN)) {
 833                         if (rankName.equalsIgnoreCase("Sectio")) { return Rank.SECTION_ZOOLOGY();
 834                         }else if (rankName.equalsIgnoreCase("Subsectio")) { return Rank.SUBSECTION_ZOOLOGY();
 835                         }
 836                 }
 837                 return getRankByName(rankName, useUnknown);
 838         }
 839
 840         /**
 841          * Returns the abbreviated rank name for <i>this</i> rank according to the English representation
 842          * abbreviated label.
 843          * TODO Needs to be changed to Latin as soon as Latin representations are available.
 844          *
 845          * @return      the abbreviation string for <i>this</i> rank
 846          */
 847         public String getAbbreviation(){
 848                 Language language = Language.ENGLISH();
 849                 String result = this.getRepresentation(language).getAbbreviatedLabel();
 850                 if (result== null) {
 851                         logger.warn("Abbreviation for this Rank " + this.toString() +  " not yet implemented");
 852                         return "no abbreviation available.";
 853                 }else{
 854                         return result;
 855                 }
 856         }
 857         @Transient
 858         public String getInfraGenericMarker() throws UnknownCdmTypeException{
 859                 String result = null;
 860                 if (! this.isInfraGeneric()){
 861                         throw new IllegalStateException("An infrageneric marker is only available for a infrageneric rank but was asked for rank: " + this.toString());
 862                 }else{
 863                         result = this.getAbbreviation();
 864                 }
 865                 if (result == null){
 866                         throw new UnknownCdmTypeException("Abbreviation for rank unknown: " + this.toString());
 867                 }
 868                 return result;
 869         }
 870
 871
 872
 873         @Override
 874         public Rank readCsvLine(Class<Rank> termClass, List<String> csvLine, Map<UUID, DefinedTermBase> terms) {
 875                 return super.readCsvLine(termClass, csvLine, terms);
 876         }
 877
 878         @Override
 879         protected void setDefaultTerms(TermVocabulary<Rank> termVocabulary) {
 880                 termMap = new HashMap<UUID, Rank>();
 881                 for (Rank term : termVocabulary.getTerms()){
 882                         termMap.put(term.getUuid(), (Rank)term);
 883                         addRank(term);
 884                 }
 885         }
 886
 887         /**
 888          * @param term
 889          */
 890         private void addRank(Rank rank) {
 891                 if (rank == null){
 892                         logger.warn("rank is NULL");
 893                         return;
 894                 }
 895                 if (rank.getUuid().equals(uuidSectionZoology) || rank.getUuid().equals(uuidSubsectionZoology )){
 896                         //sect./subsect. is used for botanical sections, see also #getRankByAbbreviation(String, NomenclaturalCode, boolean)
 897                         return;
 898                 }
 899                 Language lang = Language.DEFAULT();  //TODO should be Latin but at the moment we have only English representations
 900                 Representation representation = rank.getRepresentation(lang);
 901                 String abbrevLabel = representation.getAbbreviatedLabel();
 902                 String label = representation.getLabel();
 903                 if (abbrevLabel == null){
 904                         logger.warn("label is NULL");
 905                         return;
 906                 }
 907                 //initialize maps
 908                 if (abbrevMap == null){
 909                         abbrevMap = new HashMap<String, UUID>();
 910                 }
 911                 if (labelMap == null){
 912                         labelMap = new HashMap<String, UUID>();
 913                 }
 914                 //add to map
 915                 abbrevMap.put(abbrevLabel, rank.getUuid());
 916                 labelMap.put(label.toLowerCase(), rank.getUuid());
 917         }
 918
 919
 920         /**
 921          * It is nessecary to skip the vocabulary check, otherwise we would have
 922          * problems in some CacheStrategies, due to uninitialized Vocabularies.
 923          *
 924          * @see eu.etaxonomy.cdm.model.common.OrderedTermBase#compareTo(eu.etaxonomy.cdm.model.common.OrderedTermBase)
 925          */
 926         @Override
 927         public int compareTo(Rank orderedTerm) {
 928                 return performCompareTo(orderedTerm, true);
 929         }
 930
 931 }