Package | Description |
---|---|
eu.etaxonomy.cdm.api.service.config | |
eu.etaxonomy.cdm.api.service.lsid | |
eu.etaxonomy.cdm.api.service.lsid.impl | |
eu.etaxonomy.cdm.ext.openurl | |
eu.etaxonomy.cdm.jaxb | |
eu.etaxonomy.cdm.model.agent |
Provides classes for different kinds of agents such as persons, teams or
institutions.
|
eu.etaxonomy.cdm.model.common |
Provides general technical or common classes on the base of which
are built the model classes of all others thematic packages.
|
eu.etaxonomy.cdm.model.description |
Provides classes:
to describe specimens, observations or taxa,
to associate other factual informations to specimens, observations or taxa (including distribution),
to supply additional information about taxon names and
to support identification by means of keys.
Related documentation
UML Diagrams |
eu.etaxonomy.cdm.model.location |
Provides classes for georeferencing gathering or observation events.
|
eu.etaxonomy.cdm.model.media | |
eu.etaxonomy.cdm.model.molecular |
Provides classes for DNA samples and related sequences.
|
eu.etaxonomy.cdm.model.name |
Provides classes for nomenclature and typification.
|
eu.etaxonomy.cdm.model.occurrence |
Provides classes for specimens, collections and field units.
|
eu.etaxonomy.cdm.model.reference |
Provides classes for nomenclatural and bibliographical references
either as a complex structure of specific subclasses according to the different kind of possible references used (see StrictReferenceBase class and subclasses)
or as a flat structure (see BibTexReference class).
Related documentation
UML Diagrams |
eu.etaxonomy.cdm.model.taxon |
Provides classes for taxonomy including synonymy and concept synonymy.
|
eu.etaxonomy.cdm.model.term | |
eu.etaxonomy.cdm.persistence.dao.common | |
eu.etaxonomy.cdm.persistence.dao.hibernate.common | |
eu.etaxonomy.cdm.strategy.cache.common |
Modifier and Type | Class and Description |
---|---|
class |
IdentifiableServiceConfiguratorImpl<T extends IIdentifiableEntity> |
interface |
IIdentifiableEntityServiceConfigurator<T extends IIdentifiableEntity> |
Modifier and Type | Method and Description |
---|---|
static <T extends IIdentifiableEntity> |
IdentifiableServiceConfiguratorFactory.getConfigurator(java.lang.Class<T> clazz) |
Modifier and Type | Interface and Description |
---|---|
interface |
LSIDMetadataMapper<T extends IIdentifiableEntity>
Class which takes an Identifiable entity of type T and transforms it into
an object graph which can be marshalled into an xml document.
|
Modifier and Type | Method and Description |
---|---|
IIdentifiableEntity |
LSIDMetadataService.getMetadata(LSID lsid)
Get the meta data associated with the LSID
|
Modifier and Type | Method and Description |
---|---|
IIdentifiableEntity |
LsidMetadataServiceImpl.getMetadata(LSID lsid) |
Modifier and Type | Class and Description |
---|---|
class |
OpenUrlReference |
Modifier and Type | Method and Description |
---|---|
java.lang.Class<? extends IIdentifiableEntity> |
Namespace.getClazz() |
java.util.Map<java.lang.String,java.lang.Class<? extends IIdentifiableEntity>> |
NamespacesAdapter.unmarshal(NamespacesElement value) |
Modifier and Type | Method and Description |
---|---|
NamespacesElement |
NamespacesAdapter.marshal(java.util.Map<java.lang.String,java.lang.Class<? extends IIdentifiableEntity>> value) |
void |
Namespace.setClazz(java.lang.Class<? extends IIdentifiableEntity> clazz) |
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 |
AnnotationType
Annotation types ...
|
class |
ExtensionType
Extension types similar to dynamically defined attributes.
|
class |
IdentifiableEntity<S extends IIdentifiableEntityCacheStrategy>
Superclass for the primary CDM classes that can be referenced from outside via LSIDs and contain a simple generated title string as a label for human reading.
|
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 |
---|---|
java.util.Map<java.lang.String,java.lang.Class<? extends IIdentifiableEntity>> |
LSIDAuthority.getNamespaces() |
Modifier and Type | Method and Description |
---|---|
void |
LSIDAuthority.addNamespace(java.lang.String namespace,
java.lang.Class<? extends IIdentifiableEntity> identifiableClass) |
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 | 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 |
INonViralName |
interface |
ITaxonName |
interface |
ITaxonNameBase
The upmost interface for taxon names.
|
interface |
IViralName
The taxon name interface for viral taxa.
|
interface |
IZoologicalName
TaxonName interface for animals.
|
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 | Interface and Description |
---|---|
interface |
IArticle
This interface represents articles in a
journal . |
interface |
IAuthoredPublicationBase
Interface for all publications that are published at a certain date in time
and a have an author.
|
interface |
IBook
This interface represents books.
|
interface |
IBookSection
This interface represents isolated sections (parts or chapters) within a
book or proceedings . |
interface |
ICdDvd
This interface represents electronic publications the support of which are Cds
(Compact Discs) or Dvds (Digital Versatile Discs).
|
interface |
IDatabase
This interface represents a database used as an information source.
|
interface |
IGeneric
This interface represents all references which cannot be clearly assigned to a
particular
reference subclass. |
interface |
IInProceedings
This interface represents isolated parts (usually papers or abstracts) within
conference proceedings . |
interface |
IJournal
This interface represents journals.
|
interface |
IMap
This interface represents published maps from which information can be derived.
|
interface |
INomenclaturalReference
Interface providing methods for nomenclatural references.
|
interface |
IPatent
This interface represents patents.
|
interface |
IPersonalCommunication
This interface represents personal communications.
|
interface |
IPrintedUnitBase
This interface represents printed
published references which
are recurrent products of publishing companies or of research organizations. |
interface |
IPrintSeries
This interface represents collections of
printed published references which
are grouped according to topic or any other feature. |
interface |
IProceedings
This interface represents conference proceedings.
|
interface |
IPublicationBase
This base interface represents all different kind of published
references which constitute a physical
or virtual unit. |
interface |
IReference
The upmost interface for references (information sources).
|
interface |
IReport
This interface represents reports.
|
interface |
ISection
This interface represents isolated sections (parts, chapters or
papers) within a
printed unit . |
interface |
IThesis
This interface represents a thesis.
|
interface |
IVolumeReference
Interface for all references that support set/getVolume().
|
interface |
IWebPage
This interface represents electronic publications available on the world wide web.
|
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 | Method and Description |
---|---|
java.lang.Class<? extends IIdentifiableEntity> |
ILsidAuthorityDao.getClassForNamespace(LSID lsid) |
Modifier and Type | Method and Description |
---|---|
java.lang.Class<? extends IIdentifiableEntity> |
LsidAuthorityDaoImpl.getClassForNamespace(LSID lsid) |
Modifier and Type | Interface and Description |
---|---|
interface |
IIdentifiableEntityCacheStrategy<T extends IIdentifiableEntity>
Base interface for formatting of
identifiable entities . |
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