Package | Description |
---|---|
eu.etaxonomy.cdm.api.service | |
eu.etaxonomy.cdm.io.common | |
eu.etaxonomy.cdm.io.common.utils | |
eu.etaxonomy.cdm.io.markup | |
eu.etaxonomy.cdm.io.taxonx2013 | |
eu.etaxonomy.cdm.model.name |
Provides classes for nomenclature and typification.
|
eu.etaxonomy.cdm.persistence.dao.hibernate.name | |
eu.etaxonomy.cdm.persistence.dao.name | |
eu.etaxonomy.cdm.strategy.cache.name | |
eu.etaxonomy.cdm.strategy.parser | |
eu.etaxonomy.cdm.validation.constraint |
Modifier and Type | Method and Description |
---|---|
Pager<HybridRelationship> |
INameService.getHybridNames(INonViralName name,
HybridRelationshipType type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Return a List of hybrids related to this name, optionally filtered
by hybrid relationship type
|
Pager<HybridRelationship> |
NameServiceImpl.getHybridNames(INonViralName name,
HybridRelationshipType type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
protected LuceneSearch |
NameServiceImpl.prepareFindByFuzzyNameSearch(java.lang.Class<? extends CdmBase> clazz,
INonViralName nvn,
float accuracy,
int maxNoOfResults,
java.util.List<Language> languages,
boolean highlightFragments) |
Modifier and Type | Method and Description |
---|---|
protected void |
CdmImportBase.fillMissingEpithets(INonViralName parentName,
INonViralName childName)
If the child name is missing genus or species epithet information and the rank is below genus
or species respectively the according epithets are taken from the parent name.
|
Modifier and Type | Method and Description |
---|---|
<NAME extends INonViralName> |
ImportDeduplicationHelper.getExistingName(STATE state,
NAME name) |
Modifier and Type | Method and Description |
---|---|
void |
ImportDeduplicationHelper.replaceAuthorNamesAndNomRef(STATE state,
INonViralName name)
This method replaces name authors, nomenclatural reference and
nomenclatural reference author by existing authors and references
if matching authors or references exist.
|
Modifier and Type | Method and Description |
---|---|
protected INonViralName |
MarkupImportBase.createNameByCode(MarkupImportState state,
Rank rank)
Creates a
INonViralName object depending on the defined NomenclaturalCode
and the given parameters. |
Modifier and Type | Method and Description |
---|---|
protected void |
MarkupImportBase.handleFullName(MarkupImportState state,
javax.xml.stream.XMLEventReader reader,
INonViralName name,
javax.xml.stream.events.XMLEvent event) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
TaxonXExtractor.askIfReuseBestMatchingTaxon(INonViralName taxonname2,
Taxon bestMatchingTaxon,
Reference refMods,
double similarityScore,
double similarityAuthor) |
void |
TaxonXTreatmentExtractor.lookForParentNode(INonViralName taxonName,
Taxon tax,
Reference ref,
TaxonXTreatmentExtractor.MyName myName) |
Modifier and Type | Interface and Description |
---|---|
interface |
IBacterialName
TaxonName interface for bacteria.
|
interface |
IBotanicalName
TaxonName interface for plants, fungi and algae.
|
interface |
ICultivarPlantName
The TaxonName interface for cultivars (cultivated plants).
|
interface |
IFungusName
TaxonName interface for fungi.
|
interface |
ITaxonName |
interface |
IZoologicalName
TaxonName interface for animals.
|
Modifier and Type | Class and Description |
---|---|
class |
TaxonName
The upmost (abstract) class for scientific taxon names regardless of any
particular
nomenclature code . |
Modifier and Type | Method and Description |
---|---|
static INonViralName |
TaxonNameFactory.NewNonViralInstance(Rank rank,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
TeamOrPersonBase combinationAuthorship,
Reference nomenclaturalReference,
java.lang.String nomenclMicroRef,
HomotypicalGroup homotypicalGroup) |
Modifier and Type | Method and Description |
---|---|
HybridRelationship |
INonViralName.addHybridChild(INonViralName childName,
HybridRelationshipType type,
java.lang.String ruleConsidered)
Creates a new
hybrid relationship
to this non viral name. |
HybridRelationship |
TaxonName.addHybridChild(INonViralName childName,
HybridRelationshipType type,
java.lang.String ruleConsidered)
Creates a new
hybrid relationship
to this botanical name. |
HybridRelationship |
INonViralName.addHybridParent(INonViralName parentName,
HybridRelationshipType type,
Reference reference,
java.lang.String microReference,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Creates a new
hybrid relationship
to this non viral name. |
HybridRelationship |
TaxonName.addHybridParent(INonViralName parentName,
HybridRelationshipType type,
Reference reference,
java.lang.String microReference,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition) |
HybridRelationship |
INonViralName.addHybridParent(INonViralName parentName,
HybridRelationshipType type,
java.lang.String ruleConsidered)
Creates a new
hybrid relationship
to this non viral name. |
HybridRelationship |
TaxonName.addHybridParent(INonViralName parentName,
HybridRelationshipType type,
java.lang.String ruleConsidered) |
void |
INonViralName.removeHybridChild(INonViralName child) |
void |
TaxonName.removeHybridChild(INonViralName child) |
void |
INonViralName.removeHybridParent(INonViralName parent) |
void |
TaxonName.removeHybridParent(INonViralName parent) |
void |
HybridRelationship.setHybridName(INonViralName hybridName) |
void |
HybridRelationship.setParentName(INonViralName parentName) |
protected void |
HybridRelationship.setRelatedFrom(INonViralName relatedFrom) |
protected void |
HybridRelationship.setRelatedTo(INonViralName relatedTo) |
Constructor and Description |
---|
HybridRelationship(INonViralName hybridName,
INonViralName parentName,
HybridRelationshipType type,
Reference citation,
java.lang.String citationMicroReference,
java.lang.String ruleConsidered,
NomenclaturalCodeEdition codeEdition)
Class constructor: creates a new hybrid relationship instance including
its
reference source and adds it to the respective
botanical taxon name relation sets of both involved names. |
HybridRelationship(INonViralName hybridName,
INonViralName parentName,
HybridRelationshipType type,
java.lang.String ruleConsidered)
Class constructor: creates a new hybrid relationship instance with no
reference and adds it to the respective
botanical taxon name relation sets of both involved names. |
Modifier and Type | Method and Description |
---|---|
int |
TaxonNameDaoHibernateImpl.countHybridNames(INonViralName name,
HybridRelationshipType type) |
java.util.List<HybridRelationship> |
TaxonNameDaoHibernateImpl.getHybridNames(INonViralName name,
HybridRelationshipType type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Modifier and Type | Method and Description |
---|---|
int |
ITaxonNameDao.countHybridNames(INonViralName name,
HybridRelationshipType type)
Return a count of hybrids related to this name, optionally filtered by
hybrid relationship type
|
java.util.List<HybridRelationship> |
ITaxonNameDao.getHybridNames(INonViralName name,
HybridRelationshipType type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Return a List of hybrids related to this name, optionally filtered by
hybrid relationship type
|
Modifier and Type | Method and Description |
---|---|
protected void |
TaxonNameDefaultCacheStrategy.addAppendedTaggedPhrase(java.util.List<TaggedText> tags,
INonViralName nonViralName)
Adds the tag for the appended phrase if an appended phrase exists
|
protected void |
TaxonNameDefaultCacheStrategy.addInfraGenericPart(INonViralName name,
java.util.List<TaggedText> tags,
java.lang.String infraGenericMarker,
java.lang.String infraGenEpi)
Default implementation for the infrageneric part of a name.
|
protected void |
ZooNameNoMarkerCacheStrategy.addInfraGenericPart(INonViralName name,
java.util.List<TaggedText> tags,
java.lang.String infraGenericMarker,
java.lang.String infraGenEpi) |
protected java.util.List<TaggedText> |
TaxonNameDefaultCacheStrategy.getGenusOrUninomialTaggedNameCache(INonViralName nonViralName)
Returns the tag list for an genus or higher taxon.
|
protected java.util.List<TaggedText> |
TaxonNameDefaultCacheStrategy.getInfraGenusTaggedNameCache(INonViralName nonViralName)
Returns the tag list for an infrageneric taxon (including species aggregates).
|
protected java.util.List<TaggedText> |
TaxonNameDefaultCacheStrategy.getInfraSpeciesTaggedNameCache(INonViralName nonViralName,
boolean includeMarker)
Creates the tag list for an infraspecific taxon.
|
protected java.util.List<TaggedText> |
TaxonNameDefaultCacheStrategy.getRanklessTaggedNameCache(INonViralName nonViralName)
Returns the tag list for rankless taxa.
|
protected java.util.List<TaggedText> |
TaxonNameDefaultCacheStrategy.getSpeciesAggregateTaggedCache(INonViralName nonViralName)
Returns the tag list for a species aggregate (or similar) taxon.
Possible ranks for a species aggregate are "aggr.", "species group", ... |
protected java.util.List<TaggedText> |
TaxonNameDefaultCacheStrategy.getSpeciesTaggedNameCache(INonViralName nonViralName)
Returns the tag list for a species taxon.
|
protected boolean |
TaxonNameDefaultCacheStrategy.nameIncludesAuthorship(INonViralName nonViralName)
Checks if the given name should include the author in it's cached version.
This is usually the case but not for species aggregates. |
Modifier and Type | Interface and Description |
---|---|
interface |
INonViralNameParser<T extends INonViralName>
Supplies several parser methods for non viral taxon name strings and for nomenclatural
reference strings.
|
Modifier and Type | Method and Description |
---|---|
INonViralName |
NonViralNameParserImpl.getNonViralNameInstance(java.lang.String fullString,
NomenclaturalCode code) |
INonViralName |
NonViralNameParserImpl.getNonViralNameInstance(java.lang.String fullString,
NomenclaturalCode code,
Rank rank) |
INonViralName |
NonViralNameParserImpl.parseFullName(java.lang.String fullNameString) |
INonViralName |
NonViralNameParserImpl.parseFullName(java.lang.String fullNameString,
NomenclaturalCode nomCode,
Rank rank) |
INonViralName |
NonViralNameParserImpl.parseSimpleName(java.lang.String simpleName) |
INonViralName |
NonViralNameParserImpl.parseSimpleName(java.lang.String simpleName,
NomenclaturalCode code,
Rank rank) |
Modifier and Type | Method and Description |
---|---|
void |
NonViralNameParserImpl.handleAuthors(INonViralName nameToBeFilled,
java.lang.String fullNameString,
java.lang.String authorString) |
void |
NonViralNameParserImpl.parseAuthors(INonViralName nonViralNameOrig,
java.lang.String authorString)
Author parser for external use
|
void |
INonViralNameParser.parseAuthors(INonViralName nonViralName,
java.lang.String authorString) |
void |
NonViralNameParserImpl.parseFullName(INonViralName nameToBeFilledOrig,
java.lang.String fullNameStringOrig,
Rank rank,
boolean makeEmpty) |
java.lang.String |
NonViralNameParserImpl.parseNomStatus(java.lang.String fullString,
INonViralName nameToBeFilled,
boolean makeEmpty)
Extracts a
NomenclaturalStatus from the reference String and adds it to the @link TaxonName . |
void |
NonViralNameParserImpl.parseReferencedName(INonViralName nameToBeFilled,
java.lang.String fullReferenceStringOrig,
Rank rank,
boolean makeEmpty) |
void |
NonViralNameParserImpl.parseSimpleName(INonViralName nameToBeFilled,
java.lang.String simpleNameString,
Rank rank,
boolean makeEmpty) |
Modifier and Type | Method and Description |
---|---|
boolean |
MustHaveAuthorityValidator.isValid(INonViralName name,
javax.validation.ConstraintValidatorContext constraintContext) |
boolean |
CorrectEpithetsForRankValidator.isValid(INonViralName name,
javax.validation.ConstraintValidatorContext constraintContext) |
Copyright © 2007-2020 EDIT. All Rights Reserved.