Modifier and Type | Method and Description |
---|---|
Pager<TaxonBase> |
TaxonServiceImpl.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonBase> |
ITaxonService.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
Pager<TaxonNameParts> |
INameService.findTaxonNameParts(java.util.Optional<java.lang.String> genusOrUninomial,
java.util.Optional<java.lang.String> infraGenericEpithet,
java.util.Optional<java.lang.String> specificEpithet,
java.util.Optional<java.lang.String> infraSpecificEpithet,
Rank rank,
java.util.Set<java.util.UUID> excludedNamesUuids,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<OrderHint> orderHints)
Supports using wildcards in the query parameters.
|
Pager<TaxonNameParts> |
NameServiceImpl.findTaxonNameParts(java.util.Optional<java.lang.String> genusOrUninomial,
java.util.Optional<java.lang.String> infraGenericEpithet,
java.util.Optional<java.lang.String> specificEpithet,
java.util.Optional<java.lang.String> infraSpecificEpithet,
Rank rank,
java.util.Set<java.util.UUID> excludedNamesUuids,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<OrderHint> orderHints) |
java.util.List<GroupedTaxonDTO> |
IClassificationService.groupTaxaByHigherTaxon(java.util.List<java.util.UUID> taxonUuids,
java.util.UUID classificationUuid,
Rank minRank,
Rank maxRank)
Returns the higher taxon id for each taxon in taxonUuids.
|
java.util.List<GroupedTaxonDTO> |
ClassificationServiceImpl.groupTaxaByHigherTaxon(java.util.List<java.util.UUID> originalTaxonUuids,
java.util.UUID classificationUuid,
Rank minRank,
Rank maxRank) |
java.util.List<TaxonNode> |
IClassificationService.listRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths)
Loads all TaxonNodes of the specified classification for a given Rank or lower.
|
java.util.List<TaxonNode> |
ClassificationServiceImpl.listRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonBase> |
TaxonServiceImpl.listTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonBase> |
ITaxonService.listTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
java.util.List<TaxonNode> |
IClassificationService.loadTreeBranch(TaxonNode taxonNode,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
ClassificationServiceImpl.loadTreeBranch(TaxonNode taxonNode,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
IClassificationService.loadTreeBranch(TaxonNode taxonNode,
TaxonNode subtree,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
ClassificationServiceImpl.loadTreeBranch(TaxonNode taxonNode,
TaxonNode subtree,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
IClassificationService.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
ClassificationServiceImpl.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNode> |
IClassificationService.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
TaxonNode subtree,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths)
Although this method seems to be a redundant alternative to
IClassificationService.loadChildNodesOfTaxonNode(TaxonNode, List) it is an important
alternative from which web services benefit. |
java.util.List<TaxonNode> |
ClassificationServiceImpl.loadTreeBranchToTaxon(Taxon taxon,
Classification classification,
TaxonNode subtree,
Rank baseRank,
boolean includeUnpublished,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonNode> |
IClassificationService.pageRankSpecificRootNodes(Classification classification,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths)
Deprecated.
keep this for compatibility to older versions, might be removed in versions >5.3
|
Pager<TaxonNode> |
ClassificationServiceImpl.pageRankSpecificRootNodes(Classification classification,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonNode> |
IClassificationService.pageRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths)
Loads all TaxonNodes of the specified classification for a given Rank or lower.
|
Pager<TaxonNode> |
ClassificationServiceImpl.pageRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
Rank rank,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<java.lang.String> propertyPaths) |
Pager<TaxonName> |
INameService.searchNames(java.lang.String uninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a List of TaxonName instances that match the properties passed
|
Pager<TaxonName> |
NameServiceImpl.searchNames(java.lang.String uninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
FIXME Candidate for harmonization
rename search
|
java.util.List<TaxonNodeDto> |
TaxonNodeServiceImpl.taxonNodeDtoParentRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
java.util.List<TaxonNodeDto> |
ITaxonNodeService.taxonNodeDtoParentRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
java.util.List<TaxonNodeDto> |
TaxonNodeServiceImpl.taxonNodeDtoParentRank(Classification classification,
Rank rank,
TaxonName name) |
java.util.List<TaxonNodeDto> |
ITaxonNodeService.taxonNodeDtoParentRank(Classification classification,
Rank rank,
TaxonName name) |
Modifier and Type | Method and Description |
---|---|
void |
TaxonDistributionDTO.setRank(Rank rank) |
Constructor and Description |
---|
TaxonNamePartsFilter(Rank rank,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
java.util.Set<TaxonName> exludedNames) |
Modifier and Type | Method and Description |
---|---|
java.util.List<IBotanicalName> |
IpniService.getNamesAdvanced(java.lang.String family,
java.lang.String genus,
java.lang.String species,
java.lang.String infraFamily,
java.lang.String infraGenus,
java.lang.String infraSpecies,
java.lang.String authorAbbrev,
java.lang.String publicationTitle,
Rank rankInRangeToReturn,
IpniServiceNamesConfigurator config,
ICdmRepository services) |
java.util.List<IBotanicalName> |
IIpniService.getNamesAdvanced(java.lang.String family,
java.lang.String genus,
java.lang.String species,
java.lang.String infraFamily,
java.lang.String infraGenus,
java.lang.String infraSpecies,
java.lang.String authorAbbrev,
java.lang.String publicationTitle,
Rank rankRangeToReturn,
IpniServiceNamesConfigurator config,
ICdmRepository repository)
As
#getNamesAdvanced(String, String, String, String, String, String, String, Boolean, Boolean, String, Boolean, Boolean, Boolean, IpniRank, Boolean, IpniServiceNamesConfigurator, ICdmRepository)
but using CDM Rank instead of IpniRank. |
static IpniService.IpniRank |
IpniService.IpniRank.valueOf(Rank rank) |
Modifier and Type | Method and Description |
---|---|
LogicFilter<Rank> |
TaxonNodeFilter.getRankMax() |
LogicFilter<Rank> |
TaxonNodeFilter.getRankMin() |
Modifier and Type | Method and Description |
---|---|
static TaxonNodeFilter |
TaxonNodeFilter.NewRankInstance(Rank rankMin,
Rank rankMax) |
TaxonNodeFilter |
TaxonNodeFilter.setRankMax(Rank rankMax) |
TaxonNodeFilter |
TaxonNodeFilter.setRankMin(Rank rankMin) |
Constructor and Description |
---|
TaxonNodeFilter(Rank rankMin,
Rank rankMax) |
Modifier and Type | Method and Description |
---|---|
static Rank |
BerlinModelTransformer.rankId2Rank(java.sql.ResultSet rs,
boolean useUnknown,
boolean switchSpeciesGroup) |
Modifier and Type | Method and Description |
---|---|
static java.lang.Integer |
BerlinModelTransformer.rank2RankId(Rank rank) |
Modifier and Type | Method and Description |
---|---|
protected Rank |
CdmImportBase.getRank(STATE state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
OrderedTermVocabulary<Rank> voc,
Rank lowerRank,
RankClass rankClass) |
Rank |
ImportStateBase.getRank(java.util.UUID uuid) |
Modifier and Type | Method and Description |
---|---|
protected Rank |
CdmImportBase.getRank(STATE state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
OrderedTermVocabulary<Rank> voc,
Rank lowerRank,
RankClass rankClass) |
void |
ImportStateBase.putRank(Rank rank) |
Modifier and Type | Method and Description |
---|---|
protected Rank |
CdmImportBase.getRank(STATE state,
java.util.UUID uuid,
java.lang.String label,
java.lang.String text,
java.lang.String labelAbbrev,
OrderedTermVocabulary<Rank> voc,
Rank lowerRank,
RankClass rankClass) |
Modifier and Type | Method and Description |
---|---|
Rank |
InputTransformerBase.getRankByKey(java.lang.String key) |
Rank |
IInputTransformer.getRankByKey(java.lang.String key) |
Modifier and Type | Method and Description |
---|---|
Rank |
CsvNameExportConfigurator.getRank() |
Modifier and Type | Method and Description |
---|---|
void |
CsvNameExportConfigurator.setRank(Rank rank) |
Modifier and Type | Method and Description |
---|---|
protected java.lang.String |
CsvDemoRecordBase.getRank(Rank rank) |
static java.lang.String |
CsvDemoExportTransformer.transformToGbifRank(Rank term) |
Modifier and Type | Method and Description |
---|---|
protected java.lang.String |
CsvRecordBaseRedlist.getRank(Rank rank) |
static java.lang.String |
CsvTaxExportTransformerRedlist.transformToGbifRank(Rank term) |
Modifier and Type | Method and Description |
---|---|
Rank |
DwcaTypesRecord.getTaxonRank() |
Rank |
DwcaTaxonRecord.getTaxonRank() |
Modifier and Type | Method and Description |
---|---|
protected java.lang.String |
DwcaRecordBase.getRank(Rank rank) |
void |
DwcaTypesRecord.setTaxonRank(Rank taxonRank) |
void |
DwcaTaxonRecord.setTaxonRank(Rank taxonRank) |
static java.lang.String |
DwcaTaxExportTransformer.transformToGbifRank(Rank term) |
Modifier and Type | Method and Description |
---|---|
protected Rank |
MarkupImportBase.makeRank(MarkupImportState state,
java.lang.String value,
boolean byAbbrev) |
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 TaxonName |
SpecimenImportBase.getOrCreateTaxonName(java.lang.String scientificName,
Rank rank,
boolean preferredFlag,
STATE state,
int unitIndexInAbcdFile) |
protected TaxonName |
SpecimenImportBase.parseScientificName(java.lang.String scientificName,
STATE state,
SpecimenImportReport report,
Rank rank)
Parse automatically the scientific name
|
Modifier and Type | Method and Description |
---|---|
static Rank |
TaxonXTransformer.rankString2Rank(java.lang.String strRank)
Creates an cdm-Rank by the tcs rank
|
Modifier and Type | Method and Description |
---|---|
protected Rank |
TaxonXExtractor.askForRank(java.lang.String fullname,
Rank rank,
NomenclaturalCode nomenclaturalCode) |
Rank |
TaxonXTreatmentExtractor.MyName.getHigherRank() |
Rank |
TaxonXImportConfigurator.getMaxRank() |
Rank |
TaxonXTreatmentExtractor.MyName.getRank() |
protected Rank |
TaxonXExtractor.getRank(java.util.Map<java.lang.String,java.lang.String> ato) |
protected Rank |
TaxonXExtractor.getRank(java.lang.String r) |
Modifier and Type | Method and Description |
---|---|
protected Rank |
TaxonXExtractor.askForRank(java.lang.String fullname,
Rank rank,
NomenclaturalCode nomenclaturalCode) |
Taxon |
TaxonXTreatmentExtractor.MyName.findOrCreateTaxon(java.lang.String partialname,
java.lang.String fullname,
Rank rank,
Rank globalrank) |
void |
TaxonXTreatmentExtractor.MyName.setHigherRank(Rank higherRank) |
void |
TaxonXImportConfigurator.setMaxRank(Rank maxRank) |
void |
TaxonXTreatmentExtractor.MyName.setRank(Rank rank) |
Modifier and Type | Method and Description |
---|---|
static Rank |
TcsRdfTransformer.rankString2Rank(java.lang.String strRank)
Creates an cdm-Rank by the tcs rank
|
Modifier and Type | Method and Description |
---|---|
static Rank |
TcsXmlTransformer.rankCode2Rank(java.lang.String strRank)
Creates an cdm-Rank by the tcs rank
|
static Rank |
TcsXmlTransformer.rankString2Rank(java.lang.String strRank) |
Modifier and Type | Method and Description |
---|---|
protected static Rank |
TcsXmlTaxonNameImport.makeRank(org.jdom.Element elRank)
Returns the rank represented by the rank element.
Returns null if the element is null.Returns null if the code and the text are both either empty or do not exists.Returns the rank represented by the code attribute, if the code attribute is not empty and could be resolved. If the code could not be resolved it returns the rank represented most likely by the elements text. Returns UNKNOWN_RANK if code attribute and element text could not be resolved. |
Modifier and Type | Method and Description |
---|---|
Rank |
DescriptiveDataSet.getMaxRank() |
Rank |
DescriptiveDataSet.getMinRank() |
Modifier and Type | Method and Description |
---|---|
void |
DescriptiveDataSet.setMaxRank(Rank maxRank) |
void |
DescriptiveDataSet.setMinRank(Rank minRank) |
Modifier and Type | Field and Description |
---|---|
protected static java.util.Map<java.util.UUID,Rank> |
Rank.termMap |
Modifier and Type | Method and Description |
---|---|
static Rank |
Rank.BIOVARIETY() |
static Rank |
Rank.CANDIDATE() |
static Rank |
Rank.CLASS() |
static Rank |
Rank.CONVAR() |
static Rank |
Rank.CULTIVAR() |
static Rank |
Rank.CULTIVARGROUP() |
static Rank |
Rank.DENOMINATIONCLASS() |
static Rank |
Rank.DIVISION() |
static Rank |
Rank.DOMAIN() |
static Rank |
Rank.EMPIRE() |
static Rank |
Rank.FAMILY() |
static Rank |
Rank.FORM() |
static Rank |
Rank.GENUS() |
Rank |
TaxonName.getRank()
Returns the taxonomic
rank of this taxon name. |
Rank |
ITaxonNameBase.getRank()
Returns the taxonomic
rank of this taxon name. |
static Rank |
Rank.getRankByEnglishName(java.lang.String rankName,
NomenclaturalCode nc,
boolean useUnknown)
Defines the rank according to the English name.
|
static Rank |
Rank.getRankByIdInVoc(java.lang.String abbrev)
Returns the rank identified through the vocabulary identifier.
|
static Rank |
Rank.getRankByIdInVoc(java.lang.String idInVoc,
boolean useUnknown)
Returns the rank identified through an abbreviated representation.
|
static Rank |
Rank.getRankByIdInVoc(java.lang.String abbrev,
NomenclaturalCode nc)
Returns the rank identified through an abbreviated name for a given nomenclatural code.
|
static Rank |
Rank.getRankByIdInVoc(java.lang.String abbrev,
NomenclaturalCode nc,
boolean useUnknown)
Returns the rank identified through an abbreviated name for a given nomenclatural code.
|
static Rank |
Rank.getRankByName(java.lang.String rankName)
Returns the rank identified through a name.
|
static Rank |
Rank.getRankByName(java.lang.String rankName,
boolean useUnknown)
Returns the rank identified through a name.
|
static Rank |
Rank.getRankByName(java.lang.String rankName,
NomenclaturalCode nc)
Returns the rank identified through a name for a given nomenclatural code.
|
static Rank |
Rank.getRankByName(java.lang.String rankName,
NomenclaturalCode nc,
boolean useUnknown) |
static Rank |
Rank.getRankByNameOrIdInVoc(java.lang.String strRank)
Returns the rank identified through a label or the identifier within the vocabulary
Preliminary implementation for BotanicalNameParser.
|
static Rank |
Rank.getRankByNameOrIdInVoc(java.lang.String strRank,
boolean useUnknown)
Returns the rank identified through a label or the identifier within the vocabulary.
|
static Rank |
Rank.getRankByNameOrIdInVoc(java.lang.String strRank,
NomenclaturalCode nc)
Returns the rank identified through a label or the identifier within the vocabulary
for a given nomenclatural code.
|
static Rank |
Rank.getRankByNameOrIdInVoc(java.lang.String strRank,
NomenclaturalCode nc,
boolean useUnknown)
Returns the rank identified through a label or the identifier within the vocabulary.
|
protected static Rank |
Rank.getTermByUuid(java.util.UUID uuid) |
static Rank |
Rank.GRAFTCHIMAERA() |
static Rank |
Rank.GREX() |
static Rank |
Rank.INFRACLASS() |
static Rank |
Rank.INFRADIVISION() |
static Rank |
Rank.INFRAFAMILY() |
static Rank |
Rank.INFRAGENERICTAXON()
'Unranked infrageneric'.
|
static Rank |
Rank.INFRAGENUS() |
static Rank |
Rank.INFRAKINGDOM() |
static Rank |
Rank.INFRAORDER() |
static Rank |
Rank.INFRAPHYLUM() |
static Rank |
Rank.INFRASPECIES() |
static Rank |
Rank.INFRASPECIFICTAXON()
'Unranked infraspecific'.
|
static Rank |
Rank.INFRATRIBE() |
static Rank |
Rank.KINGDOM() |
static Rank |
Rank.NATIO() |
static Rank |
Rank.NewInstance(RankClass rankClass,
java.lang.String term,
java.lang.String label,
java.lang.String labelAbbrev)
Creates an additional rank with a description (in the
default language ),
a label and a label abbreviation. |
static Rank |
Rank.ORDER() |
static Rank |
Rank.PATHOVARIETY() |
static Rank |
Rank.PHYLUM() |
static Rank |
Rank.PROLES() |
static Rank |
Rank.RACE() |
Rank |
Rank.readCsvLine(java.lang.Class<Rank> termClass,
java.util.List<java.lang.String> csvLine,
TermType termType,
java.util.Map<java.util.UUID,DefinedTermBase> terms,
boolean abbrevAsId) |
static Rank |
Rank.SECTION_BOTANY() |
static Rank |
Rank.SECTION_ZOOLOGY() |
static Rank |
Rank.SERIES() |
static Rank |
Rank.SPECIALFORM() |
static Rank |
Rank.SPECIES() |
static Rank |
Rank.SPECIESAGGREGATE() |
static Rank |
Rank.SPECIESGROUP() |
static Rank |
Rank.SUBCLASS() |
static Rank |
Rank.SUBDIVISION() |
static Rank |
Rank.SUBFAMILY() |
static Rank |
Rank.SUBFORM() |
static Rank |
Rank.SUBGENUS() |
static Rank |
Rank.SUBKINGDOM() |
static Rank |
Rank.SUBLUSUS() |
static Rank |
Rank.SUBORDER() |
static Rank |
Rank.SUBPHYLUM() |
static Rank |
Rank.SUBSECTION_BOTANY() |
static Rank |
Rank.SUBSECTION_ZOOLOGY() |
static Rank |
Rank.SUBSERIES() |
static Rank |
Rank.SUBSPECIES() |
static Rank |
Rank.SUBSPECIFICAGGREGATE() |
static Rank |
Rank.SUBSUBFORM() |
static Rank |
Rank.SUBSUBVARIETY() |
static Rank |
Rank.SUBTRIBE() |
static Rank |
Rank.SUBVARIETY() |
static Rank |
Rank.SUPERCLASS() |
static Rank |
Rank.SUPERDIVISION() |
static Rank |
Rank.SUPERFAMILY() |
static Rank |
Rank.SUPERKINGDOM() |
static Rank |
Rank.SUPERORDER() |
static Rank |
Rank.SUPERPHYLUM() |
static Rank |
Rank.SUPERTRIBE() |
static Rank |
Rank.SUPRAGENERICTAXON() |
static Rank |
Rank.TRIBE() |
static Rank |
Rank.UNKNOWN_RANK() |
static Rank |
Rank.UNRANKED_INFRAGENERIC() |
static Rank |
Rank.UNRANKED_INFRASPECIFIC() |
static Rank |
Rank.VARIETY() |
Modifier and Type | Method and Description |
---|---|
int |
Rank.compareTo(Rank orderedTerm)
It is necessary to skip the vocabulary check, otherwise we would have
problems in some CacheStrategies, due to uninitialized Vocabularies.
|
TaxonName |
NomenclaturalCode.getNewTaxonNameInstance(Rank rank)
Creates a new particular
taxon name (botanical, zoological,
cultivar plant, bacterial or viral name) instance depending on this
nomenclature code only containing the given rank . |
static TaxonName |
TaxonNameFactory.NewBacterialInstance(Rank rank)
Creates a new bacterial taxon name instance
only containing its
rank and
the default cache strategy . |
static IBacterialName |
TaxonNameFactory.NewBacterialInstance(Rank rank,
HomotypicalGroup homotypicalGroup)
Creates a new bacterial taxon name instance
only containing its
rank ,
its homotypical group and
the default cache strategy . |
static TaxonName |
TaxonNameFactory.NewBotanicalInstance(Rank rank)
Creates a new botanical taxon name instance
only containing its
rank and
the default cache strategy . |
static TaxonName |
TaxonNameFactory.NewBotanicalInstance(Rank rank,
HomotypicalGroup homotypicalGroup)
Creates a new botanical taxon name instance
only containing its
rank ,
its homotypical group and
the default cache strategy . |
static TaxonName |
TaxonNameFactory.NewBotanicalInstance(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)
Creates a new botanical taxon name instance
containing its
rank ,
its homotypical group ,
its scientific name components, its author(team) ,
its nomenclatural reference and
the default cache strategy . |
static TaxonName |
TaxonNameFactory.NewCultivarInstance(Rank rank)
Creates a new cultivar taxon name instance
only containing its
rank and
the default cache strategy . |
static ICultivarPlantName |
TaxonNameFactory.NewCultivarInstance(Rank rank,
HomotypicalGroup homotypicalGroup)
Creates a new cultivar taxon name instance
only containing its
rank ,
its homotypical group and
the default cache strategy . |
static TaxonName |
TaxonNameFactory.NewFungusInstance(Rank rank) |
protected static TaxonName |
TaxonName.NewInstance(NomenclaturalCode code,
Rank rank,
HomotypicalGroup homotypicalGroup) |
static TaxonName |
TaxonName.NewInstance(NomenclaturalCode code,
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) |
static TaxonName |
TaxonNameFactory.NewNameInstance(NomenclaturalCode code,
Rank rank)
|
static TaxonName |
TaxonNameFactory.NewNameInstance(NomenclaturalCode code,
Rank rank,
HomotypicalGroup homotypicalGroup)
|
static TaxonName |
TaxonNameFactory.NewNonViralInstance(Rank rank)
Creates a new non viral taxon name instance
only containing its
rank and
the default cache strategy . |
static TaxonName |
TaxonNameFactory.NewNonViralInstance(Rank rank,
HomotypicalGroup homotypicalGroup)
Creates a new non viral taxon name instance
only containing its
rank ,
its homotypical group and
the default cache strategy . |
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) |
static TaxonName |
TaxonNameFactory.NewViralInstance(Rank rank)
Creates a new viral taxon name instance only containing its
rank . |
static TaxonName |
TaxonNameFactory.NewZoologicalInstance(Rank rank)
Creates a new zoological taxon name instance
only containing its
rank and
the default cache strategy . |
static TaxonName |
TaxonNameFactory.NewZoologicalInstance(Rank rank,
HomotypicalGroup homotypicalGroup)
Creates a new zoological taxon name instance
only containing its
rank ,
its homotypical group and
the default cache strategy . |
static TaxonName |
TaxonNameFactory.NewZoologicalInstance(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)
Creates a new zoological taxon name instance
containing its
rank ,
its homotypical group ,
its scientific name components, its author(team) ,
its nomenclatural reference and
the default cache strategy . |
static IBotanicalName |
TaxonNameFactory.PARSED_BOTANICAL_REFERENCE(java.lang.String fullNameAndReferenceString,
Rank rank)
Returns a botanical taxon name based on parsing a string representing
all elements (according to the ICBN) of a botanical taxon name including
authorship and nomenclatural reference.
|
static TaxonName |
TaxonNameFactory.PARSED_BOTANICAL(java.lang.String fullNameString,
Rank rank)
Returns a botanical taxon name based on parsing a string representing
all elements (according to the ICBN) of a botanical taxon name including
authorship but without nomenclatural reference.
|
static TaxonName |
TaxonNameFactory.PARSED_ZOOLOGICAL(java.lang.String fullNameString,
Rank rank)
Returns a zoological taxon name based on parsing a string representing
all elements (according to the
ICZN )) of a zoological taxon name including
authorship but without nomenclatural reference. |
void |
TaxonName.setRank(Rank rank) |
void |
ITaxonNameBase.setRank(Rank rank) |
Modifier and Type | Method and Description |
---|---|
Rank |
Rank.readCsvLine(java.lang.Class<Rank> termClass,
java.util.List<java.lang.String> csvLine,
TermType termType,
java.util.Map<java.util.UUID,DefinedTermBase> terms,
boolean abbrevAsId) |
protected void |
Rank.setDefaultTerms(TermVocabulary<Rank> termVocabulary) |
Constructor and Description |
---|
TaxonName(NomenclaturalCode type,
Rank rank,
HomotypicalGroup homotypicalGroup)
Class constructor: creates a new taxon name instance
only containing its
rank and
its homotypical group and
the default cache strategy . |
TaxonName(NomenclaturalCode type,
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)
Class constructor: creates a new non viral taxon name instance
containing its
rank ,
its homotypical group ,
its scientific name components, its author(team) ,
its nomenclatural reference and
the default cache strategy . |
Modifier and Type | Method and Description |
---|---|
Rank |
TaxonBase.getNullSafeRank() |
Rank |
TaxonNode.getNullSafeRank() |
Modifier and Type | Method and Description |
---|---|
TaxonNode |
TaxonNode.getAncestorOfRank(Rank rank)
Retrieves the first ancestor of the given rank.
|
Modifier and Type | Method and Description |
---|---|
long |
TaxonNameDaoHibernateImpl.countNames(java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
Rank rank) |
long |
TaxonNameDaoHibernateImpl.countTaxonNameParts(java.util.Optional<java.lang.String> genusOrUninomial,
java.util.Optional<java.lang.String> infraGenericEpithet,
java.util.Optional<java.lang.String> specificEpithet,
java.util.Optional<java.lang.String> infraSpecificEpithet,
Rank rank,
java.util.Collection<java.util.UUID> excludedNamesUUIDs)
Count method complementing
#findTaxonNameParts(Optional, Optional, Optional, Optional, Rank) |
java.util.List<TaxonNameParts> |
TaxonNameDaoHibernateImpl.findTaxonNameParts(java.util.Optional<java.lang.String> genusOrUninomial,
java.util.Optional<java.lang.String> infraGenericEpithet,
java.util.Optional<java.lang.String> specificEpithet,
java.util.Optional<java.lang.String> infraSpecificEpithet,
Rank rank,
java.util.Collection<java.util.UUID> excludedNamesUuids,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<OrderHint> orderHints)
Supports using wildcards in the query parameters.
|
java.util.List<TaxonName> |
TaxonNameDaoHibernateImpl.searchNames(java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
Rank rank,
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 |
---|---|
long[] |
ClassificationDaoHibernateImpl.countRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
Rank rank) |
long |
TaxonDaoHibernateImpl.countTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
java.lang.String authorshipCache,
Rank rank) |
java.util.List<TaxonBase> |
TaxonDaoHibernateImpl.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet,
java.lang.String authorship,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonNodeDto> |
TaxonNodeDaoHibernateImpl.getParentTaxonNodeDtoForRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
java.util.List<TaxonNodeDto> |
TaxonNodeDaoHibernateImpl.getParentTaxonNodeDtoForRank(Classification classification,
Rank rank,
TaxonName name) |
java.util.List<TaxonNode> |
ClassificationDaoHibernateImpl.listRankSpecificRootNodes(Classification classification,
TaxonNode taxonNode,
Rank rank,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths,
int queryIndex) |
Modifier and Type | Method and Description |
---|---|
protected java.util.List<TaxonName> |
AbstractHibernateTaxonGraphProcessor.listNamesAtRank(Rank rank,
java.lang.String genusOrUninomial,
java.lang.String specificEpithet) |
protected java.util.List<TaxonName> |
AbstractHibernateTaxonGraphProcessor.listNamesBelowRank(Rank rank,
java.lang.String genusOrUninomial,
java.lang.String specificEpithet) |
Modifier and Type | Method and Description |
---|---|
long |
ITaxonNameDao.countNames(java.lang.String uninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
Rank rank)
Returns a count of TaxonName instances that match the properties
passed
|
long |
ITaxonNameDao.countTaxonNameParts(java.util.Optional<java.lang.String> genusOrUninomial,
java.util.Optional<java.lang.String> infraGenericEpithet,
java.util.Optional<java.lang.String> specificEpithet,
java.util.Optional<java.lang.String> infraSpecificEpithet,
Rank rank,
java.util.Collection<java.util.UUID> excludedNames)
Count method complementing
#findTaxonNameParts(Optional, Optional, Optional, Optional, Rank) |
java.util.List<TaxonNameParts> |
ITaxonNameDao.findTaxonNameParts(java.util.Optional<java.lang.String> genusOrUninomial,
java.util.Optional<java.lang.String> infraGenericEpithet,
java.util.Optional<java.lang.String> specificEpithet,
java.util.Optional<java.lang.String> infraSpecificEpithet,
Rank rank,
java.util.Collection<java.util.UUID> excludedNamesUuids,
java.lang.Integer pageSize,
java.lang.Integer pageIndex,
java.util.List<OrderHint> orderHints)
Supports using wildcards in the query parameters.
|
java.util.List<TaxonName> |
ITaxonNameDao.searchNames(java.lang.String uninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a List of TaxonName instances that match the properties
passed
|
Modifier and Type | Method and Description |
---|---|
long[] |
IClassificationDao.countRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
boolean includeUnpublished,
Rank rank) |
long |
ITaxonDao.countTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank)
Returns a count of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
java.util.List<TaxonBase> |
ITaxonDao.findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
java.util.List<TaxonNodeDto> |
ITaxonNodeDao.getParentTaxonNodeDtoForRank(Classification classification,
Rank rank,
TaxonBase<?> taxonBase) |
java.util.List<TaxonNodeDto> |
ITaxonNodeDao.getParentTaxonNodeDtoForRank(Classification classification,
Rank rank,
TaxonName name) |
java.util.List<TaxonNode> |
IClassificationDao.listRankSpecificRootNodes(Classification classification,
TaxonNode subtree,
Rank rank,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<java.lang.String> propertyPaths,
int queryIndex)
Lists all TaxonNodes of the specified tree for a given Rank.
|
Modifier and Type | Field and Description |
---|---|
protected Rank |
TaxonNameParts.rank |
Modifier and Type | Method and Description |
---|---|
Rank |
SortableTaxonNodeQueryResult.getNameRank() |
Rank |
TaxonNameParts.getRank() |
Modifier and Type | Method and Description |
---|---|
java.util.Map<Rank,java.util.Set<java.lang.Integer>> |
ClassificationLookupDTO.getTaxonIdByRank() |
Modifier and Type | Method and Description |
---|---|
void |
ClassificationLookupDTO.add(java.lang.Integer taxonId,
Rank rank,
java.lang.Integer parentId) |
void |
ClassificationLookupDTO.dropRank(Rank rank) |
void |
SortableTaxonNodeQueryResult.setNameRank(Rank nameRank) |
void |
TaxonNameParts.setRank(Rank rank) |
Modifier and Type | Method and Description |
---|---|
void |
ClassificationLookupDTO.filterInclude(java.util.List<Rank> includeRanks)
Drops all ranks from the classifiacationLookupDTO except those
listed in ranks.
|
Constructor and Description |
---|
SortableTaxonNodeQueryResult(java.util.UUID taxonNodeUuid,
java.lang.Integer taxonNodeId,
java.lang.String taxonTitleCache,
Rank nameRank)
Is this the reason
|
TaxonNameParts(java.lang.Integer taxonNameId,
java.util.UUID taxonNameUuid,
Rank rank,
java.lang.String genusOrUninomial,
java.lang.String infraGenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraSpecificEpithet) |
Modifier and Type | Method and Description |
---|---|
Pager<TaxonNodeAgentRelation> |
AgentController.doGetTaxonNodeAgentRelations(java.util.UUID uuid,
java.util.UUID classificationUuid,
java.util.UUID taxonUuid,
java.util.UUID relTypeUuid,
Rank rank,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response)
See also
TaxonController#doGetTaxonNodeAgentRelations(UUID, UUID, Integer, Integer, HttpServletRequest, HttpServletResponse) |
Modifier and Type | Method and Description |
---|---|
INonViralName |
NonViralNameParserImpl.getNonViralNameInstance(java.lang.String fullString,
NomenclaturalCode code,
Rank rank) |
void |
NonViralNameParserImpl.parseFullName(INonViralName nameToBeFilledOrig,
java.lang.String fullNameStringOrig,
Rank rank,
boolean makeEmpty) |
INonViralName |
NonViralNameParserImpl.parseFullName(java.lang.String fullNameString,
NomenclaturalCode nomCode,
Rank rank) |
T |
INonViralNameParser.parseFullName(java.lang.String fullName,
NomenclaturalCode nomCode,
Rank rank)
Parses the taxon name String and returns a TaxonName.
|
void |
INonViralNameParser.parseFullName(T nameToBeFilled,
java.lang.String fullName,
Rank rank,
boolean makeEmpty)
Parses the taxon name String and fills the result into the existing TaxonName nameToBeFilled.
|
void |
NonViralNameParserImpl.parseReferencedName(INonViralName nameToBeFilled,
java.lang.String fullReferenceStringOrig,
Rank rank,
boolean makeEmpty) |
TaxonName |
NonViralNameParserImpl.parseReferencedName(java.lang.String fullReferenceString,
NomenclaturalCode nomCode,
Rank rank) |
T |
INonViralNameParser.parseReferencedName(java.lang.String fullReference,
NomenclaturalCode nomCode,
Rank rank) |
void |
INonViralNameParser.parseReferencedName(T nameToBeFilled,
java.lang.String fullReference,
Rank rank,
boolean makeEmpty)
Parses a String (fullReference) assuming that it represents a taxonomic name, it's reference,
and it's nomenclatural status.
Status: First the last part of the string is checked if it represents a nomenclatural status (e.g. |
void |
NonViralNameParserImpl.parseSimpleName(INonViralName nameToBeFilled,
java.lang.String simpleNameString,
Rank rank,
boolean makeEmpty) |
INonViralName |
NonViralNameParserImpl.parseSimpleName(java.lang.String simpleName,
NomenclaturalCode code,
Rank rank) |
T |
INonViralNameParser.parseSimpleName(java.lang.String simpleName,
NomenclaturalCode code,
Rank rank)
Parses the taxon name String and returns a TaxonName.
|
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