2 * Copyright (C) 2007 EDIT
3 * European Distributed Institute of Taxonomy
4 * http://www.e-taxonomy.eu
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.
10 package eu
.etaxonomy
.cdm
.model
.name
;
12 import java
.util
.HashMap
;
13 import java
.util
.List
;
15 import java
.util
.UUID
;
17 import javax
.persistence
.Entity
;
18 import javax
.persistence
.Transient
;
19 import javax
.validation
.constraints
.NotNull
;
20 import javax
.xml
.bind
.annotation
.XmlAccessType
;
21 import javax
.xml
.bind
.annotation
.XmlAccessorType
;
22 import javax
.xml
.bind
.annotation
.XmlAttribute
;
23 import javax
.xml
.bind
.annotation
.XmlType
;
25 import org
.apache
.commons
.lang
.StringUtils
;
26 import org
.apache
.log4j
.Logger
;
27 import org
.hibernate
.annotations
.Type
;
28 import org
.hibernate
.envers
.Audited
;
29 import org
.hibernate
.search
.annotations
.Indexed
;
31 import eu
.etaxonomy
.cdm
.common
.CdmUtils
;
32 import eu
.etaxonomy
.cdm
.model
.common
.DefinedTermBase
;
33 import eu
.etaxonomy
.cdm
.model
.common
.Language
;
34 import eu
.etaxonomy
.cdm
.model
.common
.OrderedTermBase
;
35 import eu
.etaxonomy
.cdm
.model
.common
.Representation
;
36 import eu
.etaxonomy
.cdm
.model
.common
.TermType
;
37 import eu
.etaxonomy
.cdm
.model
.common
.TermVocabulary
;
38 import eu
.etaxonomy
.cdm
.strategy
.exceptions
.UnknownCdmTypeException
;
41 * The class representing the taxonomical ranks (like "Family", "Genus" or
42 * "Species") used for {@link TaxonNameBase taxon names} across all {@link NomenclaturalCode nomenclatural codes}
43 * for bacteria (ICNB), viruses (ICVCN), plants and fungi (ICBN),
44 * cultivars (ICNCP) and animals (ICZN).
46 * A standard (ordered) list of taxonomical rank instances will be automatically
47 * created as the project starts. But this class allows to extend this standard
48 * list by creating new instances of additional taxonomical ranks if needed.
50 * This class corresponds to: <ul>
51 * <li> TaxonRankTerm according to the TDWG ontology
52 * <li> TaxonomicRankEnum according to the TCS
53 * <li> Rank according to the ABCD schema
58 * @created 08-Nov-2007 13:06:46
60 @XmlAccessorType(XmlAccessType
.FIELD
)
61 @XmlType(name
= "Rank")
63 @Indexed(index
= "eu.etaxonomy.cdm.model.common.DefinedTermBase")
65 public class Rank
extends OrderedTermBase
<Rank
> {
66 private static final long serialVersionUID
= -8648081681348758485L;
67 private static final Logger logger
= Logger
.getLogger(Rank
.class);
69 private static final UUID uuidEmpire
= UUID
.fromString("ac470211-1586-4b24-95ca-1038050b618d");
70 private static final UUID uuidDomain
= UUID
.fromString("ffca6ec8-8b88-417b-a6a0-f7c992aac19b");
71 private static final UUID uuidSuperkingdom
= UUID
.fromString("64223610-7625-4cfd-83ad-b797bf7f0edd");
72 private static final UUID uuidKingdom
= UUID
.fromString("fbe7109d-66b3-498c-a697-c6c49c686162");
73 private static final UUID uuidSubkingdom
= UUID
.fromString("a71bd9d8-f3ab-4083-afb5-d89315d71655");
74 private static final UUID uuidInfrakingdom
= UUID
.fromString("1e37930c-86cf-44f6-90fd-7822928df260");
75 private static final UUID uuidSuperphylum
= UUID
.fromString("0d0cecb1-e254-4607-b210-6801e7ecbb04");
76 private static final UUID uuidPhylum
= UUID
.fromString("773430d2-76b4-438c-b817-97a543a33287");
77 private static final UUID uuidSubphylum
= UUID
.fromString("23a9b6ff-9408-49c9-bd9e-7a2ca5ab4725");
78 private static final UUID uuidInfraphylum
= UUID
.fromString("1701de3a-7693-42a5-a2d3-42697f944190");
79 private static final UUID uuidSuperdivision
= UUID
.fromString("a735a48f-4fc8-49a7-ae0c-6a984f658131");
80 private static final UUID uuidDivision
= UUID
.fromString("7e56f5cc-123a-4fd1-8cbb-6fd80358b581");
81 private static final UUID uuidSubdivision
= UUID
.fromString("931c840f-7a6b-4d76-ad38-bfdd77d7b2e8");
82 private static final UUID uuidInfradivision
= UUID
.fromString("c0ede273-be52-4dee-b411-66ee08d30c94");
83 private static final UUID uuidSuperclass
= UUID
.fromString("e65b4e1a-21ec-428d-9b9f-e87721ab967c");
84 private static final UUID uuidClass
= UUID
.fromString("f23d14c4-1d34-4ee6-8b4e-eee2eb9a3daf");
85 private static final UUID uuidSubclass
= UUID
.fromString("8cb26733-e2f5-46cb-ab5c-f99254f877aa");
86 private static final UUID uuidInfraclass
= UUID
.fromString("ad23cfda-879a-4021-8629-c54d27caf717");
87 private static final UUID uuidSuperorder
= UUID
.fromString("c8c67a22-301a-4219-b882-4a49121232ff");
88 private static final UUID uuidOrder
= UUID
.fromString("b0785a65-c1c1-4eb4-88c7-dbd3df5aaad1");
89 private static final UUID uuidSuborder
= UUID
.fromString("768ad378-fa85-42ab-b668-763225832f57");
90 private static final UUID uuidInfraorder
= UUID
.fromString("84099182-a6f5-47d7-8586-33c9e9955a10");
91 private static final UUID uuidSectionZoology
= UUID
.fromString("691d371e-10d7-43f0-93db-3d7fa1a62c54");
92 private static final UUID uuidSubsectionZoology
= UUID
.fromString("0ed32d28-adc4-4303-a9ca-68e2acd67e33");
93 private static final UUID uuidSuperfamily
= UUID
.fromString("2cfa510a-dcea-4a03-b66a-b1528f9b0796");
94 private static final UUID uuidFamily
= UUID
.fromString("af5f2481-3192-403f-ae65-7c957a0f02b6");
95 private static final UUID uuidSubfamily
= UUID
.fromString("862526ee-7592-4760-a23a-4ff3641541c5");
96 private static final UUID uuidInfrafamily
= UUID
.fromString("c3f2e3bb-6eef-4a26-9fb7-b14f4c8c5e4f");
97 private static final UUID uuidSupertribe
= UUID
.fromString("11e94828-8c61-499b-87d6-1de35ce2c51c");
98 private static final UUID uuidTribe
= UUID
.fromString("4aa6890b-0363-4899-8d7c-ee0cb78e6166");
99 private static final UUID uuidSubtribe
= UUID
.fromString("ae41ecc5-5165-4126-9d24-79939ae5d822");
100 private static final UUID uuidInfratribe
= UUID
.fromString("1ec02e8f-f2b7-4c65-af9f-b436b34c79a3");
101 private static final UUID uuidSupragenericTaxon
= UUID
.fromString("1fdc0b93-c354-441a-8406-091e0303ff5c");
102 public static final UUID uuidGenus
= UUID
.fromString("1b11c34c-48a8-4efa-98d5-84f7f66ef43a");
103 private static final UUID uuidSubgenus
= UUID
.fromString("78786e16-2a70-48af-a608-494023b91904");
104 private static final UUID uuidInfragenus
= UUID
.fromString("a9972969-82cd-4d54-b693-a096422f13fa");
105 private static final UUID uuidSectionBotany
= UUID
.fromString("3edff68f-8527-49b5-bf91-7e4398bb975c");
106 private static final UUID uuidSubsectionBotany
= UUID
.fromString("d20f5b61-d463-4448-8f8a-c1ff1f262f59");
107 private static final UUID uuidSeries
= UUID
.fromString("d7381ecf-48f8-429b-9c54-f461656978cd");
108 private static final UUID uuidSubseries
= UUID
.fromString("80c9a263-f4db-4a13-b6c2-b7fec1aa1200");
109 private static final UUID uuidSpeciesAggregate
= UUID
.fromString("1ecae058-4217-4f75-9c27-6d8ba099ac7a");
110 private static final UUID uuidSpeciesGroup
= UUID
.fromString("d1988a11-292b-46fa-8fb7-bc64ea6d8fc6");
111 public static final UUID uuidInfragenericTaxon
= UUID
.fromString("41bcc6ac-37d3-4fd4-bb80-3cc5b04298b9");
112 public static final UUID uuidSpecies
= UUID
.fromString("b301f787-f319-4ccc-a10f-b4ed3b99a86d");
113 private static final UUID uuidSubspecificAggregate
= UUID
.fromString("72c248b9-027d-4402-b375-dd4f0850c9ad");
114 private static final UUID uuidSubspecies
= UUID
.fromString("462a7819-8b00-4190-8313-88b5be81fad5");
115 private static final UUID uuidInfraspecies
= UUID
.fromString("f28ebc9e-bd50-4194-9af1-42f5cb971a2c");
116 private static final UUID uuidNatio
= UUID
.fromString("965f2f38-7f97-4270-ab5a-1999bf050a22");
117 private static final UUID uuidVariety
= UUID
.fromString("d5feb6a5-af5c-45ef-9878-bb4f36aaf490");
118 private static final UUID uuidBioVariety
= UUID
.fromString("a3a364cb-1a92-43fc-a717-3c44980a0991");
119 private static final UUID uuidPathoVariety
= UUID
.fromString("2f4f4303-a099-47e3-9048-d749d735423b");
120 private static final UUID uuidSubvariety
= UUID
.fromString("9a83862a-7aee-480c-a98d-4bceaf8712ca");
121 private static final UUID uuidSubsubvariety
= UUID
.fromString("bff22f84-553a-4429-a4e7-c4b3796c3a18");
123 private static final UUID uuidProles
= UUID
.fromString("8810d1ba-6a34-4ae3-a355-919ccd1cd1a5");
124 private static final UUID uuidRace
= UUID
.fromString("196dee39-cfd8-4460-8bf0-88b83da27f62");
125 private static final UUID uuidSublusus
= UUID
.fromString("1fafa596-a8e7-4e62-a378-3cc8cb3627ca");
127 private static final UUID uuidConvar
= UUID
.fromString("2cc740c9-cebb-43c8-9b06-1bef79e6a56a");
128 private static final UUID uuidForm
= UUID
.fromString("0461281e-458a-47b9-8d41-19a3d39356d5");
129 private static final UUID uuidSpecialForm
= UUID
.fromString("bed20aee-2f5a-4635-9c02-eff06246d067");
130 private static final UUID uuidSubform
= UUID
.fromString("47cfc5b0-0fb7-4ceb-b61d-e1dd8de8b569");
131 private static final UUID uuidSubsubform
= UUID
.fromString("1c8ac389-4349-4ae0-87be-7239f6635068");
132 public static final UUID uuidInfraspecificTaxon
= UUID
.fromString("eb75c27d-e154-4570-9d96-227b2df60474");
133 private static final UUID uuidCandidate
= UUID
.fromString("ead9a1f5-dfd4-4de2-9121-70a47accb10b");
134 private static final UUID uuidDenominationClass
= UUID
.fromString("49bdf74a-2170-40ed-8be2-887a0db517bf");
135 private static final UUID uuidGrex
= UUID
.fromString("08dcb4ff-ac58-48a3-93af-efb3d836ac84");
136 private static final UUID uuidGraftChimaera
= UUID
.fromString("6b4063bc-f934-4796-9bf3-0ef3aea5c1cb");
137 private static final UUID uuidCultivarGroup
= UUID
.fromString("d763e7d3-e7de-4bb1-9d75-225ca6948659");
138 private static final UUID uuidCultivar
= UUID
.fromString("5e98415b-dc6e-440b-95d6-ea33dbb39ad0");
139 private static final UUID uuidUnknownRank
= UUID
.fromString("5c4d6755-2cf6-44ca-9220-cccf8881700b");
141 private static Map
<String
, UUID
> idInVocMap
= null;
142 private static Map
<String
, UUID
> labelMap
= null;
144 protected static Map
<UUID
, Rank
> termMap
= null;
146 //*********************** Factory methods ********************************************/
149 // * Creates a new empty rank.
151 // * @see #NewInstance(String, String, String)
153 // private static Rank NewInstance(){
154 // return new Rank();
158 * Creates an additional rank with a description (in the {@link Language#DEFAULT() default language}),
159 * a label and a label abbreviation.
161 * @param term the string (in the default language) describing the
162 * new rank to be created
163 * @param label the string identifying the new rank to be created
164 * @param labelAbbrev the string identifying (in abbreviated form) the
165 * new rank to be created
166 * @see #NewInstance()
168 public static Rank
NewInstance(RankClass rankClass
, String term
, String label
, String labelAbbrev
){
169 return new Rank(rankClass
, term
, label
, labelAbbrev
);
173 * The {@link RankClass rank class} of a rank. It is usually needed for correct formatting of a
174 * rank by using e.g. isSupraGeneric(). Prior to v3.3 this was computed by comparison of ranks.
176 @XmlAttribute(name
="RankClass")
178 @Type(type
= "eu.etaxonomy.cdm.hibernate.EnumUserType",
179 parameters
= {@org.hibernate
.annotations
.Parameter(name
="enumClass", value
="eu.etaxonomy.cdm.model.name.RankClass")}
181 private RankClass rankClass
;
184 //********************************** Constructor *********************************/
186 //for hibernate use only
189 super(TermType
.Rank
);
193 * Class constructor: creates an additional rank instance with a description
194 * (in the {@link eu.etaxonomy.cdm.model.common.Language#DEFAULT() default language}), a label and a label abbreviation.
196 * @param term the string (in the default language) describing the
197 * new rank to be created
198 * @param label the string identifying the new rank to be created
199 * @param labelAbbrev the string identifying (in abbreviated form) the
200 * new rank to be created
203 protected Rank(RankClass rankClass
, String term
, String label
, String labelAbbrev
) {
204 super(TermType
.Rank
, term
, label
, labelAbbrev
);
205 this.rankClass
= rankClass
;
209 //********* METHODS **************************************/
212 * @see eu.etaxonomy.cdm.model.common.DefinedTermBase#resetTerms()
215 public void resetTerms(){
221 protected static Rank
getTermByUuid(UUID uuid
){
222 if (termMap
== null){
223 return null; //better return null then initialize the termMap in an unwanted way
225 return (Rank
)termMap
.get(uuid
);
228 public static final Rank
EMPIRE(){
229 return getTermByUuid(uuidEmpire
);
231 public static final Rank
DOMAIN(){
232 return getTermByUuid(uuidDomain
);
234 public static final Rank
SUPERKINGDOM(){
235 return getTermByUuid(uuidSuperkingdom
);
237 public static final Rank
KINGDOM(){
238 return getTermByUuid(uuidKingdom
);
240 public static final Rank
SUBKINGDOM(){
241 return getTermByUuid(uuidSubkingdom
);
243 public static final Rank
INFRAKINGDOM(){
244 return getTermByUuid(uuidInfrakingdom
);
246 public static final Rank
SUPERPHYLUM(){
247 return getTermByUuid(uuidSuperphylum
);
249 public static final Rank
PHYLUM(){
250 return getTermByUuid(uuidPhylum
);
252 public static final Rank
SUBPHYLUM(){
253 return getTermByUuid(uuidSubphylum
);
255 public static final Rank
INFRAPHYLUM(){
256 return getTermByUuid(uuidInfraphylum
);
258 public static final Rank
SUPERDIVISION(){
259 return getTermByUuid(uuidSuperdivision
);
261 public static final Rank
DIVISION(){
262 return getTermByUuid(uuidDivision
);
264 public static final Rank
SUBDIVISION(){
265 return getTermByUuid(uuidSubdivision
);
267 public static final Rank
INFRADIVISION(){
268 return getTermByUuid(uuidInfradivision
);
270 public static final Rank
SUPERCLASS(){
271 return getTermByUuid(uuidSuperclass
);
273 public static final Rank
CLASS(){
274 return getTermByUuid(uuidClass
);
276 public static final Rank
SUBCLASS(){
277 return getTermByUuid(uuidSubclass
);
279 public static final Rank
INFRACLASS(){
280 return getTermByUuid(uuidInfraclass
);
282 public static final Rank
SUPERORDER(){
283 return getTermByUuid(uuidSuperorder
);
285 public static final Rank
ORDER(){
286 return getTermByUuid(uuidOrder
);
288 public static final Rank
SUBORDER(){
289 return getTermByUuid(uuidSuborder
);
291 public static final Rank
INFRAORDER(){
292 return getTermByUuid(uuidInfraorder
);
294 public static final Rank
SUPERFAMILY(){
295 return getTermByUuid(uuidSuperfamily
);
297 public static final Rank
FAMILY(){
298 return getTermByUuid(uuidFamily
);
300 public static final Rank
SUBFAMILY(){
301 return getTermByUuid(uuidSubfamily
);
303 public static final Rank
INFRAFAMILY(){
304 return getTermByUuid(uuidInfrafamily
);
306 public static final Rank
SUPERTRIBE(){
307 return getTermByUuid(uuidSupertribe
);
309 public static final Rank
TRIBE(){
310 return getTermByUuid(uuidTribe
);
312 public static final Rank
SUBTRIBE(){
313 return getTermByUuid(uuidSubtribe
);
315 public static final Rank
INFRATRIBE(){
316 return getTermByUuid(uuidInfratribe
);
318 public static final Rank
SUPRAGENERICTAXON(){
319 return getTermByUuid(uuidSupragenericTaxon
);
321 public static final Rank
GENUS(){
322 return getTermByUuid(uuidGenus
);
324 public static final Rank
SUBGENUS(){
325 return getTermByUuid(uuidSubgenus
);
327 public static final Rank
INFRAGENUS(){
328 return getTermByUuid(uuidInfragenus
);
330 public static final Rank
SECTION_BOTANY(){
331 return getTermByUuid(uuidSectionBotany
);
333 public static final Rank
SUBSECTION_BOTANY(){
334 return getTermByUuid(uuidSubsectionBotany
);
336 public static final Rank
SECTION_ZOOLOGY(){
337 return getTermByUuid(uuidSectionZoology
);
339 public static final Rank
SUBSECTION_ZOOLOGY(){
340 return getTermByUuid(uuidSubsectionZoology
);
342 public static final Rank
SERIES(){
343 return getTermByUuid(uuidSeries
);
345 public static final Rank
SUBSERIES(){
346 return getTermByUuid(uuidSubseries
);
348 public static final Rank
SPECIESAGGREGATE(){
349 return getTermByUuid(uuidSpeciesAggregate
);
351 public static final Rank
SPECIESGROUP(){
352 return getTermByUuid(uuidSpeciesGroup
);
355 * 'Unranked infrageneric'. An infrageneric rank which is on purpose not further defined.
356 * This sometimes holds for names from the 19th century.
358 public static final Rank
INFRAGENERICTAXON(){
359 return getTermByUuid(uuidInfragenericTaxon
);
361 public static final Rank
SPECIES(){
362 return getTermByUuid(uuidSpecies
);
364 public static final Rank
SUBSPECIFICAGGREGATE(){
365 return getTermByUuid(uuidSubspecificAggregate
);
367 public static final Rank
SUBSPECIES(){
368 return getTermByUuid(uuidSubspecies
);
370 public static final Rank
INFRASPECIES(){
371 return getTermByUuid(uuidInfraspecies
);
373 public static final Rank
VARIETY(){
374 return getTermByUuid(uuidVariety
);
376 public static final Rank
BIOVARIETY(){
377 return getTermByUuid(uuidBioVariety
);
379 public static final Rank
PATHOVARIETY(){
380 return getTermByUuid(uuidPathoVariety
);
382 public static final Rank
SUBVARIETY(){
383 return getTermByUuid(uuidSubvariety
);
385 public static final Rank
SUBSUBVARIETY(){
386 return getTermByUuid(uuidSubsubvariety
);
388 public static final Rank
PROLES(){
389 return getTermByUuid(uuidProles
);
391 public static final Rank
RACE(){
392 return getTermByUuid(uuidRace
);
394 public static final Rank
SUBLUSUS(){
395 return getTermByUuid(uuidSublusus
);
398 public static final Rank
CONVAR(){
399 return getTermByUuid(uuidConvar
);
401 public static final Rank
FORM(){
402 return getTermByUuid(uuidForm
);
404 public static final Rank
SPECIALFORM(){
405 return getTermByUuid(uuidSpecialForm
);
407 public static final Rank
SUBFORM(){
408 return getTermByUuid(uuidSubform
);
410 public static final Rank
SUBSUBFORM(){
411 return getTermByUuid(uuidSubsubform
);
414 * 'Unranked infraspecific'. An infraspecific rank which is on purpose not further defined.
415 * This sometimes holds for names from the 19th century.
417 public static final Rank
INFRASPECIFICTAXON(){
418 return getTermByUuid(uuidInfraspecificTaxon
);
420 public static final Rank
CANDIDATE(){
421 return getTermByUuid(uuidCandidate
);
423 public static final Rank
DENOMINATIONCLASS(){
424 return getTermByUuid(uuidDenominationClass
);
426 public static final Rank
GREX(){
427 return getTermByUuid(uuidGrex
);
429 public static final Rank
GRAFTCHIMAERA(){
430 return getTermByUuid(uuidGraftChimaera
);
432 public static final Rank
CULTIVARGROUP(){
433 return getTermByUuid(uuidCultivarGroup
);
435 public static final Rank
CULTIVAR(){
436 return getTermByUuid(uuidCultivar
);
438 public static final Rank
UNKNOWN_RANK(){
439 return getTermByUuid(uuidUnknownRank
);
441 public static final Rank
NATIO(){
442 return getTermByUuid(uuidNatio
);
445 * @see #INFRASPECIFICTAXON()
447 public static final Rank
UNRANKED_INFRASPECIFIC(){
448 return getTermByUuid(uuidInfraspecificTaxon
);
451 * @see #INFRAGENERICTAXON()
453 public static final Rank
UNRANKED_INFRAGENERIC(){
454 return getTermByUuid(uuidInfragenericTaxon
);
457 // ************************ GETTER / SETTER **********************************/
459 public RankClass
getRankClass() {
463 public void setRankClass(RankClass rankClass
) {
464 this.rankClass
= rankClass
;
467 // ******************************** METHODS ***************************************/
470 * Returns the boolean value indicating whether <i>this</i> rank is higher than
471 * the genus rank (true) or not (false). Returns false if <i>this</i> rank is null.
474 * @see #isInfraGeneric()
476 * @see #isInfraSpecific()
479 public boolean isSupraGeneric(){
480 return this.rankClass
.equals(RankClass
.Suprageneric
); // (this.isHigher(Rank.GENUS()));
484 * Returns the boolean value indicating whether <i>this</i> rank is the genus rank
485 * (true) or not (false). Returns false if <i>this</i> rank is null.
487 * @see #isSupraGeneric()
488 * @see #isInfraGeneric()
490 * @see #isInfraSpecific()
493 public boolean isGenus(){
494 return this.rankClass
.equals(RankClass
.Genus
); // (this.equals(Rank.GENUS()));
498 * Returns the boolean value indicating whether <i>this</i> rank is higher than the
499 * species rank and lower than the genus rank (true) or not (false). Species groups or
500 * aggregates are also handled as infrageneric ranks.
501 * Returns false if <i>this</i> rank is null.
503 * @see #isSupraGeneric()
505 * @see #isSpeciesAggregate()
507 * @see #isInfraSpecific()
510 public boolean isInfraGeneric(){
511 return this.rankClass
.equals(RankClass
.Infrageneric
) || this.rankClass
.equals(RankClass
.SpeciesGroup
) ; //(this.isLower(Rank.GENUS()) && this.isHigher(Rank.SPECIES()));
515 * Returns true if this rank indicates a rank that aggregates species
516 * like species aggregates or species groups, false otherwise.
520 public boolean isSpeciesAggregate(){
521 return this.rankClass
.equals(RankClass
.SpeciesGroup
); //(this.equals(Rank.SPECIESAGGREGATE()) || (this.isLower(Rank.SPECIESAGGREGATE()) && this.isHigher(Rank.SPECIES())));
525 * Returns the boolean value indicating whether <i>this</i> rank is the species
526 * rank (true) or not (false). Returns false if <i>this</i> rank is null.
528 * @see #isSupraGeneric()
530 * @see #isInfraGeneric()
531 * @see #isInfraSpecific()
534 public boolean isSpecies(){
535 return this.rankClass
.equals(RankClass
.Species
); //(this.equals(Rank.SPECIES()));
539 * Returns the boolean value indicating whether <i>this</i> rank is lower than the
540 * species rank (true) or not (false). Returns false if <i>this</i> rank is null.
542 * @see #isSupraGeneric()
544 * @see #isInfraGeneric()
548 public boolean isInfraSpecific(){
549 return this.rankClass
.equals(RankClass
.Infraspecific
); // (this.isLower(Rank.SPECIES()));
554 * Returns the rank identified through a label or the identifier within the vocabulary
555 * Preliminary implementation for BotanicalNameParser.
557 * @param strRank the string identifying the rank
560 public static Rank
getRankByNameOrIdInVoc(String strRank
) throws UnknownCdmTypeException
{
561 return getRankByNameOrIdInVoc(strRank
, false);
565 * Returns the rank identified through a label or the identifier within the vocabulary
566 * for a given nomenclatural code.
567 * Preliminary implementation for BotanicalNameParser.
569 * @param strRank the string identifying the rank
570 * @param nc the nomenclatural code
573 public static Rank
getRankByNameOrIdInVoc(String strRank
, NomenclaturalCode nc
) throws UnknownCdmTypeException
{
574 return getRankByNameOrIdInVoc(strRank
, nc
, false);
578 // Preliminary implementation for BotanicalNameParser.
581 * Returns the rank identified through a label or the identifier within the vocabulary.
582 * Preliminary implementation for BotanicalNameParser.
584 * @param strRank the string identifying the rank
585 * @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
586 * unknown or not yet implemented
589 public static Rank
getRankByNameOrIdInVoc(String strRank
, boolean useUnknown
) throws UnknownCdmTypeException
{
591 return getRankByIdInVoc(strRank
);
592 } catch (UnknownCdmTypeException e
) {
593 return getRankByName(strRank
, useUnknown
);
598 // Preliminary implementation for BotanicalNameParser.
601 * Returns the rank identified through a label or the identifier within the vocabulary.
602 * Preliminary implementation for BotanicalNameParser.
604 * @param strRank the string identifying the rank
605 * @param nc the nomenclatural code
606 * @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
607 * unknown or not yet implemented
610 public static Rank
getRankByNameOrIdInVoc(String strRank
, NomenclaturalCode nc
, boolean useUnknown
)
611 throws UnknownCdmTypeException
{
613 return getRankByIdInVoc(strRank
, nc
);
614 } catch (UnknownCdmTypeException e
) {
615 return getRankByName(strRank
, nc
, useUnknown
);
620 * Returns the rank identified through the vocabulary identifier.
621 * Preliminary implementation for BotanicalNameParser.<BR>
622 * Note: For abbrev = "[unranked]" the result is undefined.
623 * It maybe the infrageneric unranked or the infraspecific unranked.
624 * You need to define by context which one is correct.
626 * @param abbrev the string for the name abbreviation
629 public static Rank
getRankByIdInVoc(String abbrev
) throws UnknownCdmTypeException
{
630 return getRankByIdInVoc(abbrev
, false);
634 * Returns the rank identified through an abbreviated name for a given nomenclatural code.
635 * See also {@link #getRankByIdInVoc(String, boolean)}
637 * @param abbrev the string for the name abbreviation
638 * @param nc the nomenclatural code
641 public static Rank
getRankByIdInVoc(String abbrev
, NomenclaturalCode nc
) throws UnknownCdmTypeException
{
642 return getRankByIdInVoc(abbrev
, nc
, false);
646 // Preliminary implementation for BotanicalNameParser.
649 * Returns the rank identified through an abbreviated representation.
650 * At the moment it uses the English abbreviations (being Latin because
651 * we do not have Latin representations yet.
653 * If no according abbreviation is available it throws either an UnknownCdmTypeException
654 * or an #Rank.UNKNOWN() object depending on the useUnknown flag.
656 * @param idInVoc the string for the name abbreviation
657 * @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
658 * unknown or not yet existent
661 public static Rank
getRankByIdInVoc(String idInVoc
, boolean useUnknown
) throws UnknownCdmTypeException
{
663 if (idInVoc
== null){
664 throw new NullPointerException("idInVoc is NULL in getRankByIdInVoc");
666 if (StringUtils
.isBlank(idInVoc
)){
667 //handle empty idInVoc as unknown
668 idInVoc
= "oijas34\u0155";
670 if (idInVocMap
== null){
673 idInVoc
= normalizeSectionAndSubsection(idInVoc
);
674 UUID uuid
= idInVocMap
.get(idInVoc
);
676 result
= getTermByUuid(uuid
);
681 if (idInVoc
== null){
685 logger
.info("Unknown rank name: " + idInVoc
+ ". Rank 'UNKNOWN_RANK' created instead");
686 return Rank
.UNKNOWN_RANK();
688 throw new UnknownCdmTypeException("Unknown rank abbreviation: " + idInVoc
);
693 private static String
normalizeSectionAndSubsection(String idInVoc
) {
694 if (idInVoc
.equals("sect.")){
695 return "sect.(bot.)";
696 }else if (idInVoc
.equals("subsect.")){
697 return "subsect.(bot.)";
703 // Preliminary implementation to cover Botany and Zoology.
705 * Returns the rank identified through an abbreviated name for a given nomenclatural code.
706 * Preliminary implementation for ICBN and ICZN.
707 * See also {@link #getRankByIdInVoc(String, boolean)}
710 * @param abbrev the string for the name abbreviation
711 * @param nc the nomenclatural code
712 * @param useUnknown if true the rank UNKNOWN_RANK is returned if the abbrev is
713 * unknown or not yet implemented
716 public static Rank
getRankByIdInVoc(String abbrev
, NomenclaturalCode nc
, boolean useUnknown
)
717 throws UnknownCdmTypeException
{
719 if (nc
!= null && nc
.equals(NomenclaturalCode
.ICZN
)) {
721 if (abbrev
.equalsIgnoreCase("sect.")) {
722 return Rank
.SECTION_ZOOLOGY();
723 } else if (abbrev
.equalsIgnoreCase("subsect.")) {
724 return Rank
.SUBSECTION_ZOOLOGY();
728 return getRankByIdInVoc(abbrev
, useUnknown
);
732 // Preliminary implementation for BotanicalNameParser.
735 * Returns the rank identified through a name.
736 * Preliminary implementation for BotanicalNameParser.
738 * @param rankName the string for the name of the rank
741 public static Rank
getRankByName(String rankName
) throws UnknownCdmTypeException
{
742 return getRankByName(rankName
, false);
747 // Preliminary implementation for ICBN and ICZN.
750 * Returns the rank identified through a name for a given nomenclatural code.
751 * Preliminary implementation for ICBN and ICZN.
753 * @param rankName the string for the name of the rank
754 * @param nc the nomenclatural code
757 public static Rank
getRankByName(String rankName
, NomenclaturalCode nc
) throws UnknownCdmTypeException
{
758 return getRankByName(rankName
, nc
, false);
762 * Returns the rank identified through a name.
763 * Preliminary implementation for BotanicalNameParser.
764 * TODO At the moment we do not have Latin representations yet.
766 * @param rankName the string for the name of the rank
767 * @param useUnknown if true the rank UNKNOWN_RANK is returned if the rank name is
768 * unknown or not yet implemented
771 public static Rank
getRankByName(String rankName
, boolean useUnknown
)
772 throws UnknownCdmTypeException
{
773 if (rankName
.equalsIgnoreCase("Regnum")){ return Rank
.KINGDOM();
774 }else if (rankName
.equalsIgnoreCase("Subregnum")){ return Rank
.SUBKINGDOM();
775 }else if (rankName
.equalsIgnoreCase("Phylum")){ return Rank
.PHYLUM();
776 }else if (rankName
.equalsIgnoreCase("Subphylum")){ return Rank
.SUBPHYLUM();
777 }else if (rankName
.equalsIgnoreCase("Divisio")){ return Rank
.DIVISION();
778 }else if (rankName
.equalsIgnoreCase("Subdivisio")){ return Rank
.SUBDIVISION();
779 }else if (rankName
.equalsIgnoreCase("Classis")){ return Rank
.CLASS();
780 }else if (rankName
.equalsIgnoreCase("Subclassis")){ return Rank
.SUBCLASS();
781 }else if (rankName
.equalsIgnoreCase("Superordo")){ return Rank
.SUPERORDER();
782 }else if (rankName
.equalsIgnoreCase("Ordo")){ return Rank
.ORDER();
783 }else if (rankName
.equalsIgnoreCase("Subordo")){ return Rank
.SUBORDER();
784 }else if (rankName
.equalsIgnoreCase("Familia")){ return Rank
.FAMILY();
785 }else if (rankName
.equalsIgnoreCase("Subfamilia")){ return Rank
.SUBFAMILY();
786 }else if (rankName
.equalsIgnoreCase("Tribus")){ return Rank
.TRIBE();
787 }else if (rankName
.equalsIgnoreCase("Subtribus")){ return Rank
.SUBTRIBE();
788 }else if (rankName
.equalsIgnoreCase("Genus")){ return Rank
.GENUS();
789 }else if (rankName
.equalsIgnoreCase("Subgenus")){ return Rank
.SUBGENUS();
790 }else if (rankName
.equalsIgnoreCase("Sectio")){ return Rank
.SECTION_BOTANY();
791 }else if (rankName
.equalsIgnoreCase("Subsectio")){ return Rank
.SUBSECTION_BOTANY();
792 }else if (rankName
.equalsIgnoreCase("Series")){ return Rank
.SERIES();
793 }else if (rankName
.equalsIgnoreCase("Subseries")){ return Rank
.SUBSERIES();
794 }else if (rankName
.equalsIgnoreCase("Aggregate")){ return Rank
.SPECIESAGGREGATE();
795 }else if (rankName
.equalsIgnoreCase("Speciesgroup")){ return Rank
.SPECIESGROUP();
796 }else if (rankName
.equalsIgnoreCase("Species")){ return Rank
.SPECIES();
797 }else if (rankName
.equalsIgnoreCase("Subspecies")){ return Rank
.SUBSPECIES();
798 }else if (rankName
.equalsIgnoreCase("Convarietas")){ return Rank
.CONVAR();
799 }else if (rankName
.equalsIgnoreCase("Varietas")){ return Rank
.VARIETY();
800 }else if (rankName
.equalsIgnoreCase("Subvarietas")){ return Rank
.SUBVARIETY();
801 }else if (rankName
.equalsIgnoreCase("Forma")){ return Rank
.FORM();
802 }else if (rankName
.equalsIgnoreCase("Subforma")){ return Rank
.SUBFORM();
803 }else if (rankName
.equalsIgnoreCase("Forma spec.")){ return Rank
.SPECIALFORM();
804 }else if (rankName
.equalsIgnoreCase("tax.infragen.")){ return Rank
.INFRAGENERICTAXON();
805 }else if (rankName
.equalsIgnoreCase("tax.infrasp.")){ return Rank
.INFRASPECIFICTAXON();
807 }else if (rankName
.equalsIgnoreCase("proles")){ return Rank
.PROLES();
808 }else if (rankName
.equalsIgnoreCase("race")){ return Rank
.RACE();
809 }else if (rankName
.equalsIgnoreCase("sublusus")){ return Rank
.SUBLUSUS();
811 }else if (rankName
.equalsIgnoreCase("taxon")){ return Rank
.INFRASPECIFICTAXON(); //to create the name put 'taxon' and the infraspeciesepi to the field unnamed namephrase
814 if (rankName
== null){
815 rankName
= "(null)"; //see NPE above
818 logger
.info("Unknown rank name: " + rankName
+". Rank 'UNKNOWN_RANK' created instead");
819 return Rank
.UNKNOWN_RANK();
821 throw new UnknownCdmTypeException("Unknown rank name: " + rankName
);
827 * Defines the rank according to the English name.
828 * @param rankName English rank name.
829 * @param nc Defines the handling of the section and subsection ranks. These are in different orders depending on the
830 * nomenclatural code.
831 * @param useUnknown if true, the "Unknown" rank is returned as a placeholder.
833 * @throws UnknownCdmTypeException never thrown if useUnknown is true
835 public static Rank
getRankByEnglishName(String rankName
, NomenclaturalCode nc
, boolean useUnknown
) throws UnknownCdmTypeException
{
837 if (rankName
== null){
838 throw new NullPointerException("Abbrev is NULL in getRankByAbbreviation");
840 if (labelMap
== null){
843 //handle section and subsection (not unique representations)
844 if (rankName
.equalsIgnoreCase("Section")){
845 if (nc
!= null && nc
.equals(NomenclaturalCode
.ICZN
)){ return Rank
.SECTION_ZOOLOGY();
846 }else if (nc
!= null && nc
.equals(NomenclaturalCode
.ICNAFP
)){return Rank
.SECTION_BOTANY();
848 String errorWarning
= "Section is only defined for ICZN and ICNAFP at the moment but here needed for " + ((nc
== null)?
"(null)": nc
.toString());
849 logger
.warn(errorWarning
);
850 throw new UnknownCdmTypeException (errorWarning
);
852 }else if (rankName
.equalsIgnoreCase("Subsection")){
853 if (nc
!= null && nc
.equals(NomenclaturalCode
.ICZN
)){ return Rank
.SUBSECTION_ZOOLOGY();
854 }else if (nc
!= null && nc
.equals(NomenclaturalCode
.ICNAFP
)){ return Rank
.SUBSECTION_BOTANY();
856 String errorWarning
= "Subsection is only defined for ICZN and ICBN at the moment but here needed for " + ((nc
== null)?
"(null)": nc
.toString());
857 logger
.warn(errorWarning
);
858 throw new UnknownCdmTypeException (errorWarning
);
862 rankName
= rankName
.toLowerCase();
864 UUID uuid
= labelMap
.get(rankName
);
866 result
= getTermByUuid(uuid
);
871 if (rankName
== null){
875 logger
.info("Unknown rank name: " + rankName
+ ". Rank 'UNKNOWN_RANK' created instead");
876 return Rank
.UNKNOWN_RANK();
878 throw new UnknownCdmTypeException("Unknown rank: " + rankName
);
884 public static Rank
getRankByName(String rankName
, NomenclaturalCode nc
, boolean useUnknown
)
885 throws UnknownCdmTypeException
{
887 if (nc
.equals(NomenclaturalCode
.ICZN
)) {
888 if (rankName
.equalsIgnoreCase("Sectio")) { return Rank
.SECTION_ZOOLOGY();
889 }else if (rankName
.equalsIgnoreCase("Subsectio")) { return Rank
.SUBSECTION_ZOOLOGY();
892 return getRankByName(rankName
, useUnknown
);
896 * Returns the abbreviated rank name for <i>this</i> rank according to the English representation
898 * TODO Needs to be changed to Latin as soon as Latin representations are available.
900 * @return the abbreviation string for <i>this</i> rank
902 public String
getAbbreviation(){
903 Language language
= Language
.ENGLISH();
904 String result
= this.getRepresentation(language
).getAbbreviatedLabel();
906 logger
.warn("Abbreviation for this Rank " + this.toString() + " not yet implemented");
907 return "no abbreviation available.";
913 public String
getInfraGenericMarker() throws UnknownCdmTypeException
{
914 String result
= null;
915 if (! this.isInfraGeneric()){
916 throw new IllegalStateException("An infrageneric marker is only available for a infrageneric rank but was asked for rank: " + this.toString());
918 result
= this.getAbbreviation();
921 throw new UnknownCdmTypeException("Abbreviation for rank unknown: " + this.toString());
929 public Rank
readCsvLine(Class
<Rank
> termClass
, List
<String
> csvLine
, Map
<UUID
, DefinedTermBase
> terms
, boolean abbrevAsId
) {
930 Rank rank
= super.readCsvLine(termClass
, csvLine
, terms
, abbrevAsId
);
931 RankClass rankClass
= RankClass
.getByKey(csvLine
.get(5));
932 assert rankClass
!= null: "XXXXXXXXXXXXXXXXXXXXX Rank class must not be null: " + csvLine
;
933 rank
.setRankClass(rankClass
);
938 protected void setDefaultTerms(TermVocabulary
<Rank
> termVocabulary
) {
939 termMap
= new HashMap
<UUID
, Rank
>();
940 for (Rank term
: termVocabulary
.getTerms()){
941 termMap
.put(term
.getUuid(), (Rank
)term
);
949 private void addRank(Rank rank
) {
951 logger
.warn("rank is NULL");
954 if (rank
.getUuid().equals(uuidSectionZoology
) || rank
.getUuid().equals(uuidSubsectionZoology
)){
955 //sect./subsect. is used for botanical sections, see also #getRankByAbbreviation(String, NomenclaturalCode, boolean)
958 Language lang
= Language
.DEFAULT(); //TODO should be Latin but at the moment we have only English representations
959 Representation representation
= rank
.getRepresentation(lang
);
960 String abbrevLabel
= representation
.getAbbreviatedLabel();
961 String label
= representation
.getLabel();
964 if (idInVocMap
== null){
965 idInVocMap
= new HashMap
<String
, UUID
>();
967 if (labelMap
== null){
968 labelMap
= new HashMap
<String
, UUID
>();
970 labelMap
.put(label
.toLowerCase(), rank
.getUuid());
972 if (StringUtils
.isBlank(abbrevLabel
)){
973 logger
.info("Abbreviated label for rank is NULL or empty.Can't add rank to abbrevLabel map: " + CdmUtils
.Nz(rank
.getLabel()));
975 idInVocMap
.put(abbrevLabel
, rank
.getUuid());
981 * It is necessary to skip the vocabulary check, otherwise we would have
982 * problems in some CacheStrategies, due to uninitialized Vocabularies.
984 * @see eu.etaxonomy.cdm.model.common.OrderedTermBase#compareTo(eu.etaxonomy.cdm.model.common.OrderedTermBase)
987 public int compareTo(Rank orderedTerm
) {
988 return performCompareTo(orderedTerm
, true);