Modifier and Type | Class and Description |
---|---|
class |
IdentifiableServiceBase<T extends IdentifiableEntity,DAO extends IIdentifiableDao<T>> |
interface |
IIdentifiableEntityService<T extends IdentifiableEntity> |
Modifier and Type | Method and Description |
---|---|
IdentifiableEntity<?> |
IStatisticsService.getFilterALL_DB() |
IdentifiableEntity<?> |
StatisticsServiceImpl.getFilterALL_DB() |
Modifier and Type | Method and Description |
---|---|
Pager<IdentifiableEntity> |
TaxonServiceImpl.findTaxaAndNames(IFindTaxaAndNamesConfigurator configurator) |
Pager<IdentifiableEntity> |
ITaxonService.findTaxaAndNames(IFindTaxaAndNamesConfigurator configurator)
Returns a list of IdentifiableEntity instances (in particular, TaxonName and TaxonBase instances)
that match the properties specified in the configurator.
|
java.util.List<UuidAndTitleCache<? extends IdentifiableEntity>> |
TaxonServiceImpl.findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator config) |
java.util.List<UuidAndTitleCache<? extends IdentifiableEntity>> |
ITaxonService.findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator configurator) |
Modifier and Type | Method and Description |
---|---|
java.util.List<java.lang.Class<? extends IdentifiableEntity>> |
CacheUpdaterConfigurator.getClassList() |
Modifier and Type | Method and Description |
---|---|
static CacheUpdaterConfigurator |
CacheUpdaterConfigurator.NewInstance(java.util.List<java.lang.Class<? extends IdentifiableEntity>> classList) |
Modifier and Type | Class and Description |
---|---|
class |
EntityDTO<T extends IdentifiableEntity>
DTO for any CdmBase.
|
class |
IdentifiedEntityDTO<T extends IdentifiableEntity> |
class |
MarkedEntityDTO<T extends IdentifiableEntity>
DTO for IdentifiableEntities matching a certain marker.
|
Constructor and Description |
---|
EntityDTOBase(IdentifiableEntity entity) |
Modifier and Type | Method and Description |
---|---|
IIdentifiableDao<? extends IdentifiableEntity> |
LsidRegistryImpl.lookupDAO(LSID lsid) |
Modifier and Type | Method and Description |
---|---|
org.apache.lucene.search.Query |
QueryFactory.newEntityUuidQuery(java.lang.String uuidFieldName,
IdentifiableEntity entity) |
Modifier and Type | Method and Description |
---|---|
org.apache.lucene.search.Query |
QueryFactory.newEntityUuidsQuery(java.lang.String uuidFieldName,
java.util.List<? extends IdentifiableEntity> entities)
Creates a query for searching for documents in which the field specified by
uuidFieldName
matches at least one of the uuid of the entities , the sql equivalent of this is
WHERE uuidFieldName IN (uuid_1, uuid_2, ...) . |
Modifier and Type | Method and Description |
---|---|
java.util.List<IdentifiableEntity> |
StatisticsConfigurator.getFilter() |
Modifier and Type | Method and Description |
---|---|
void |
StatisticsConfigurator.addFilter(IdentifiableEntity filterItem) |
Constructor and Description |
---|
StatisticsConfigurator(java.util.List<IdentifiableEntity> filter,
java.util.List<StatisticsTypeEnum> types) |
Modifier and Type | Class and Description |
---|---|
class |
OpenUrlReference |
Modifier and Type | Method and Description |
---|---|
protected <T extends IdentifiableEntity> |
Cdm2CdmImportBase.handlePersisted(IdentifiableEntity identifiableEntity) |
Modifier and Type | Method and Description |
---|---|
protected <T extends IdentifiableEntity> |
Cdm2CdmImportBase.handlePersisted(IdentifiableEntity identifiableEntity) |
Modifier and Type | Method and Description |
---|---|
protected static java.lang.String |
CdmExportBase.getExtension(IdentifiableEntity identifiableEntity,
java.util.UUID uuidExtensionType) |
Modifier and Type | Method and Description |
---|---|
IdentifiableEntity |
DbImportExtensionMapper.invoke(java.sql.ResultSet rs,
IdentifiableEntity identifiableEntity) |
Modifier and Type | Method and Description |
---|---|
protected boolean |
DbImportExtensionCreationMapper.addSupplement(Extension extension,
IdentifiableEntity identifiableEntity,
java.lang.String id) |
protected void |
DbImportExtensionTypeCreationMapper.handleTermWithObject(IdentifiableEntity entity,
ExtensionType extensionType) |
IdentifiableEntity |
DbImportExtensionMapper.invoke(java.sql.ResultSet rs,
IdentifiableEntity identifiableEntity) |
Modifier and Type | Method and Description |
---|---|
protected void |
ExcelTaxonOrSpecimenImportBase.handleExtensions(IdentifiableEntity<?> identifiable,
SpecimenRow row,
SpecimenCdmExcelImportState state) |
Modifier and Type | Method and Description |
---|---|
java.lang.Class<? extends IdentifiableEntity> |
IdentifierImportConfigurator.getCdmClass() |
Modifier and Type | Method and Description |
---|---|
void |
IdentifierImportConfigurator.setCdmClass(java.lang.Class<? extends IdentifiableEntity> cdmClass) |
Modifier and Type | Method and Description |
---|---|
void |
SDDDocumentBuilder.buildRepresentation(org.apache.xerces.dom.ElementImpl element,
IdentifiableEntity ie)
Builds a Representation element using an IdentifiableEntity
|
Modifier and Type | Method and Description |
---|---|
<CLASS extends IdentifiableEntity> |
StreamImportStateBase.get(java.lang.String namespace,
java.lang.String sourceKey,
java.lang.Class<CLASS> destinationClass) |
Modifier and Type | Method and Description |
---|---|
java.util.List<IdentifiableEntity> |
StreamImportStateBase.get(java.lang.String namespace,
java.lang.String sourceKey) |
Modifier and Type | Method and Description |
---|---|
void |
StreamImportStateBase.addRelatedObject(java.lang.String sourceNamespace,
java.lang.String sourceKey,
IdentifiableEntity<?> cdmEntity) |
void |
StreamImportStateBase.putMapping(java.lang.String namespace,
java.lang.Integer sourceKey,
IdentifiableEntity<?> destinationObject) |
void |
StreamImportStateBase.putMapping(java.lang.String namespace,
java.lang.String sourceKey,
IdentifiableEntity<?> destinationObject) |
Modifier and Type | Method and Description |
---|---|
void |
StreamImportStateBase.unloadPartitionStore(java.util.Map<java.lang.String,java.util.Map<java.lang.String,IdentifiableEntity>> partitionStore) |
Modifier and Type | Class and Description |
---|---|
static class |
IImportMapping.CdmKey<CLASS extends IdentifiableEntity> |
Modifier and Type | Method and Description |
---|---|
void |
DatabaseMapping.putMapping(java.lang.String namespace,
java.lang.Integer sourceKey,
IdentifiableEntity destinationObject) |
void |
IImportMapping.putMapping(java.lang.String namespace,
java.lang.Integer sourceKey,
IdentifiableEntity destinationObject)
Put the destination object with for the given namespaced identifier into the mapping.
|
void |
InMemoryMapping.putMapping(java.lang.String namespace,
java.lang.Integer sourceKey,
IdentifiableEntity destinationObject) |
void |
DatabaseMapping.putMapping(java.lang.String namespace,
java.lang.String sourceKey,
IdentifiableEntity destinationObject) |
void |
IImportMapping.putMapping(java.lang.String namespace,
java.lang.String sourceKey,
IdentifiableEntity destinationObject)
Put the destination object with for the given namespaced identifier into the mapping.
|
void |
InMemoryMapping.putMapping(java.lang.String namespace,
java.lang.String sourceKey,
IdentifiableEntity destinationObject) |
Modifier and Type | Method and Description |
---|---|
void |
DatabaseMapping.putMapping(java.lang.String namespace,
java.lang.String sourceKey,
IImportMapping.CdmKey<IdentifiableEntity<?>> cdmKey) |
void |
InMemoryMapping.putMapping(java.lang.String namespace,
java.lang.String sourceKey,
IImportMapping.CdmKey<IdentifiableEntity<?>> cdmKey) |
Constructor and Description |
---|
CdmKey(IdentifiableEntity<?> object) |
Modifier and Type | Method and Description |
---|---|
protected <T extends IdentifiableEntity> |
TcsXmlImportBase.makeReferenceType(org.jdom.Element element,
java.lang.Class<? extends T> clazz,
MapWrapper<? extends T> objectMap,
ResultWrapper<java.lang.Boolean> success) |
Modifier and Type | Class and Description |
---|---|
class |
AgentBase<S extends IIdentifiableEntityCacheStrategy<? extends AgentBase<S>>>
The upmost (abstract) class for agents such as persons, teams or institutions.
|
class |
Institution
This class represents public or private institutions.
|
class |
Person
This class represents human beings, living or dead.
It includes name parts, contact details, institutional membership ,
and other possible information such as life time period ,
taxonomic and/or geographical specialization . |
class |
Team
This class represents teams of
persons . |
class |
TeamOrPersonBase<T extends TeamOrPersonBase<T>>
The abstract class for such
agents (persons or teams ) who might also be used
for authorship of references or of taxon names . |
Modifier and Type | Class and Description |
---|---|
class |
Identifier<T extends IdentifiableEntity<?>> |
Modifier and Type | Class and Description |
---|---|
class |
AnnotationType
Annotation types ...
|
class |
ExtensionType
Extension types similar to dynamically defined attributes.
|
class |
Language
list of languages according to current internet best practices as given by IANA
or ISO codes.
|
class |
MarkerType
Marker types similar to dynamically defined attributes.
|
class |
RelationshipTermBase<T extends RelationshipTermBase<T>> |
Modifier and Type | Method and Description |
---|---|
static <T extends IdentifiableEntity<?>> |
Identifier.NewInstance(java.lang.String identifier,
DefinedTerm type) |
static <T extends IdentifiableEntity<?>> |
Identifier.NewInstance(T identifiableEntity,
java.lang.String identifier,
DefinedTerm type) |
Modifier and Type | Method and Description |
---|---|
static Extension |
Extension.NewInstance(IdentifiableEntity<?> extendedObject,
java.lang.String value,
ExtensionType extensionType)
Creates a new extension and adds it to the extended object.
|
Modifier and Type | Class and Description |
---|---|
class |
Character
A subclass of the Feature class that is meant for handling
Features/Characters for descriptions in the narrow sense of describing
an object.
|
class |
DescriptionBase<S extends IIdentifiableEntityCacheStrategy>
The upmost (abstract) class for a description as a whole (with possibly
several
elementary information data )
for a specimen , a taxon
or even a taxon name . |
class |
DescriptiveDataSet
The working set class allows the demarcation of a set of descriptions
associated with representations and a set of features and their
dependencies.
|
class |
Feature
The class for individual properties (also designed as character, type or
category) of observed phenomena able to be described or measured.
|
class |
MeasurementUnit
This class represents measurement units such as "centimeter" or "degree
celsius".
|
class |
MediaKey
The class representing single-access fixed dichotomous or polytomous authored
decision keys (as opposed to
multiple-access keys ) used to identify
specimens or observations (this means to assign taxa to). |
class |
MultiAccessKey
The class representing multi-access dynamic keys used to identify
specimens or observations (this means to assign taxa to). |
class |
NaturalLanguageTerm |
class |
PolytomousKey
This class represents a fixed single-access key (dichotomous or
polytomous) used to identify (assign a
taxon to) a specimen or observation . |
class |
PresenceAbsenceTerm
|
class |
SpecimenDescription
This class represents descriptions for
specimens or observations . |
class |
State
This class represents terms describing different states (like "oval" or
"triangular") for
features that can be described with
categorical values (like for instance shapes). |
class |
StatisticalMeasure
/**
This class represents terms describing different statistical measures (such
as "sample size", "minimum" or "average") for
features that can be
described with numerical values (like for instance weights or temperature). |
class |
TaxonDescription
This class represents descriptions that delimit or circumscribe a real taxon.
|
class |
TaxonNameDescription
This class represents all piece of information (not ruled by a
nomenclatural code )
concerning a taxon name like for instance the content of its first
publication (protolog) or a picture of this publication. |
class |
TextFormat
The class representing kinds of formats used for structuring text
(like "xml schema namespace", "rdf", or any other format).
|
Modifier and Type | Class and Description |
---|---|
class |
Country
+/- current ISO codes.
|
class |
NamedArea |
class |
NamedAreaLevel
Controlled vocabulary to differentiate levels of areas such as province, state,
etc.
|
class |
NamedAreaType
Controlled vocabulary to differentiate categories of areas
|
class |
ReferenceSystem
Reference systems for coordinates also according to OGC (Open Geographical
Consortium) The list should be extensible at runtime through configuration.
|
Modifier and Type | Class and Description |
---|---|
class |
IdentifiableMediaEntity<S extends IIdentifiableEntityCacheStrategy<?>> |
class |
Media
A
media is any kind of media that represents a media object. |
class |
RightsType |
Modifier and Type | Class and Description |
---|---|
class |
DnaSample
A DNA Sample is the extracted DNA of a given tissue sample.
|
class |
PhylogeneticTree
"A phylogenetic tree or evolutionary tree is a branching diagram or "tree" showing the
inferred evolutionary relationships among various biological species or other entities
based upon similarities and differences in their physical and/or genetic characteristics.
|
Modifier and Type | Class and Description |
---|---|
class |
HybridRelationshipType
The class representing the categories of
hybrid relationships
between a botanical taxon name used as a parent of a hybrid taxon
name and the hybrid taxon name itself. |
class |
NameRelationshipType
The class representing the categories of
taxon name relationships between
two taxon names . |
class |
NameTypeDesignationStatus
The terms in this class define the status of a
name type designation . |
class |
NomenclaturalStatusType
The class representing categories of nomenclatural status (like "invalid",
"conserved" or "novum") to qualify the use of a particular taxon name string
depending on its
nomenclatural reference (original publication),
on its nomenclatural code and on possible decisions of the corresponding
competent authorities. |
class |
Rank
The class representing the taxonomical ranks (like "Family", "Genus" or
"Species") used for
taxon names across all nomenclatural codes
for bacteria (ICNB), viruses (ICVCN), plants and fungi (ICBN),
cultivars (ICNCP) and animals (ICZN). |
class |
SpecimenTypeDesignationStatus
The class representing status (categories) of
specimen type designations
for a taxon name or a set of them. |
class |
TaxonName
The upmost (abstract) class for scientific taxon names regardless of any
particular
nomenclature code . |
class |
TypeDesignationStatusBase<T extends TypeDesignationStatusBase<T>>
The class representing status (categories) of
specimen type designations
for a taxon name or a set of them. |
Modifier and Type | Class and Description |
---|---|
class |
Collection
Instances of this class represent a collection for primary biodiversity data.
|
class |
DerivationEventType |
class |
DerivedUnit
A derived unit is regarded as derived from a field unit,
so locality and gathering related information is captured as a separate FieldUnit object
related to a specimen via a derivation event
http://www.bgbm.org/biodivinf/docs/CollectionModel/ReprintTNR.pdf
http://www.bgbm.org/biodivinf/docs/CollectionModel/
Type figures are derived units with at least a figure object in media |
class |
FieldUnit
In situ observation of a taxon in the field.
|
class |
MediaSpecimen
Instances of MediaSpecimen represent a specimen which IS a media (photo, drawing, ...).
|
class |
SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy<?>>
type figures are observations with at least a figure object in media
|
Modifier and Type | Class and Description |
---|---|
class |
Reference
The class for references (information sources).
|
Modifier and Type | Class and Description |
---|---|
class |
Classification |
class |
Synonym
|
class |
SynonymType
The class representing categories of
synonyms
(like "heterotypic synonym of"). |
class |
Taxon
|
class |
TaxonBase<S extends ITaxonCacheStrategy>
The upmost (abstract) class for the use of a
taxon name in a reference
or within a taxonomic view/treatment either as a taxon
("accepted" respectively "correct" name) or as a (junior) synonym . |
class |
TaxonRelationshipType
The class representing categories of
taxon relationships
(like "is congruent to" or "is misapplied name for"). |
Modifier and Type | Class and Description |
---|---|
class |
DefinedTerm |
class |
DefinedTermBase<T extends DefinedTermBase>
workaround for enumerations, base type according to TDWG.
|
class |
OrderedTerm |
class |
OrderedTermBase<T extends OrderedTermBase<?>> |
class |
OrderedTermVocabulary<T extends OrderedTermBase> |
class |
TermBase |
class |
TermCollection<TERM extends DefinedTermBase,REL extends TermRelationBase> |
class |
TermGraph<T extends DefinedTermBase> |
class |
TermGraphBase<TERM extends DefinedTermBase,REL extends TermRelationBase> |
class |
TermRelationshipType |
class |
TermTree<T extends DefinedTermBase>
The class to arrange
terms in a tree structure. |
class |
TermVocabulary<T extends DefinedTermBase>
A single enumeration must only contain DefinedTerm instances of one kind
(this means a subclass of DefinedTerm).
|
Modifier and Type | Interface and Description |
---|---|
interface |
IIdentifiableDao<T extends IdentifiableEntity> |
Modifier and Type | Class and Description |
---|---|
class |
IdentifiableDaoBase<T extends IdentifiableEntity> |
Modifier and Type | Method and Description |
---|---|
java.util.List<java.util.UUID> |
StatisticsDaoHibernateImpl.getTaxonTree(IdentifiableEntity filter) |
Modifier and Type | Method and Description |
---|---|
java.util.List<UuidAndTitleCache<? extends IdentifiableEntity>> |
TaxonDaoHibernateImpl.getTaxaByNameForEditor(boolean doTaxa,
boolean doSynonyms,
boolean doNamesWithoutTaxa,
boolean doMisappliedNames,
boolean doCommonNames,
boolean includeUnpublished,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
NameSearchOrder order) |
Modifier and Type | Method and Description |
---|---|
void |
TitleAndNameCacheAutoInitializer.initialize(IdentifiableEntity<?> bean) |
Modifier and Type | Method and Description |
---|---|
java.util.List<java.util.UUID> |
IStatisticsDao.getTaxonTree(IdentifiableEntity<?> filter) |
Modifier and Type | Method and Description |
---|---|
java.util.List<UuidAndTitleCache<? extends IdentifiableEntity>> |
ITaxonDao.getTaxaByNameForEditor(boolean doTaxa,
boolean doSynonyms,
boolean doNamesWithoutTaxa,
boolean doMisappliedNames,
boolean doCommonNames,
boolean includeUnpublished,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
NameSearchOrder order) |
Modifier and Type | Class and Description |
---|---|
class |
AbstractIdentifiableController<T extends IdentifiableEntity,SERVICE extends IIdentifiableEntityService<T>> |
class |
AbstractIdentifiableListController<T extends IdentifiableEntity,SERVICE extends IIdentifiableEntityService<T>> |
class |
TaxonPortalController.EntityMediaContext<T extends IdentifiableEntity> |
Modifier and Type | Method and Description |
---|---|
Pager<IdentifiableEntity> |
TaxonListController.doFind(java.lang.String query,
java.util.UUID classificationUuid,
java.util.UUID subtreeUuid,
java.util.Set<NamedArea> areas,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
java.lang.Boolean doTaxa,
java.lang.Boolean doSynonyms,
java.lang.Boolean doMisappliedNames,
java.lang.Boolean doTaxaByCommonNames,
MatchMode matchMode,
NameSearchOrder order,
java.lang.Boolean includeAuthors,
javax.servlet.http.HttpServletRequest request,
javax.servlet.http.HttpServletResponse response)
Find Taxa, Synonyms, Common Names by name, either globally or in a specific geographic area.
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractOaiPmhController<T extends IdentifiableEntity,SERVICE extends IIdentifiableEntityService<T>> |
Modifier and Type | Method and Description |
---|---|
java.lang.Class<? extends IdentifiableEntity> |
SetSpec.getSetClass() |
Modifier and Type | Method and Description |
---|---|
abstract void |
GetRecordView.constructMetadata(Metadata metadata,
IdentifiableEntity identifiableEntity) |
abstract void |
ListRecordsView.constructMetadata(Metadata metadata,
IdentifiableEntity identifiableEntity) |
Modifier and Type | Method and Description |
---|---|
void |
GetRecordView.constructMetadata(Metadata metadata,
IdentifiableEntity identifiableEntity) |
void |
ListRecordsView.constructMetadata(Metadata metadata,
IdentifiableEntity identifiableEntity) |
Modifier and Type | Method and Description |
---|---|
void |
GetRecordView.constructMetadata(Metadata metadata,
IdentifiableEntity identifiableEntity) |
Modifier and Type | Method and Description |
---|---|
void |
GetRecordView.constructMetadata(Metadata metadata,
IdentifiableEntity identifiableEntity) |
void |
ListRecordsView.constructMetadata(Metadata metadata,
IdentifiableEntity identifiableEntity) |
Modifier and Type | Class and Description |
---|---|
class |
IdentifiableEntityDefaultCacheStrategy<T extends IdentifiableEntity> |
Modifier and Type | Method and Description |
---|---|
protected IdentifiableEntity |
SpecimenDescriptionDefaultCacheStrategy.getDescriptionEntity(SpecimenDescription description) |
protected abstract IdentifiableEntity |
DescriptionBaseDefaultCacheStrategy.getDescriptionEntity(T description) |
protected IdentifiableEntity |
TaxonDescriptionDefaultCacheStrategy.getDescriptionEntity(TaxonDescription description) |
protected IdentifiableEntity |
TaxonNameDescriptionDefaultCacheStrategy.getDescriptionEntity(TaxonNameDescription description) |
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