Package | Description |
---|---|
eu.etaxonomy.cdm.ext.openurl | |
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.metadata | |
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.permission | |
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.model.validation |
Modifier and Type | Class and Description |
---|---|
class |
OpenUrlReference |
Modifier and Type | Class and Description |
---|---|
class |
Address
This class represents atomized postal addresses.
|
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 |
InstitutionalMembership
This class allows to hold one
institution to which a person
is affiliated. |
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 |
AnnotatableEntity
Abstract superclass implementing human annotations and machine markers to be assigned to CDM objects.
|
class |
Annotation |
class |
AnnotationType
Annotation types ...
|
class |
CdmBase
The base class for all CDM domain classes implementing UUIDs and bean property change event firing.
|
class |
CdmLinkBase
Base class for subclasses linking to other CDM objects.
|
class |
Credit |
class |
EventBase |
class |
Extension
This class aims to make available more "attributes" for identifiable entities
in a flexible way.
|
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 |
IdentifiableSource
This class represents an
IOriginalSource
that can be used with identifiable entity . |
class |
Identifier<T extends IdentifiableEntity<?>> |
class |
IntextReference
This class represents a link to another CDM Base class from within a text.
|
class |
Language
list of languages according to current internet best practices as given by IANA
or ISO codes.
|
class |
LanguageString
This class is an instantiatable class for the base class
LanguageStringBase . |
class |
LanguageStringBase |
class |
LSIDAuthority |
class |
Marker
This class aims to make available some "flags" for identifiable entities in a
flexible way.
|
class |
MarkerType
Marker types similar to dynamically defined attributes.
|
class |
ReferencedEntityBase
Abstract class for all objects that may have a reference
|
class |
RelationshipBase<FROM extends IRelated,TO extends IRelated,TYPE extends RelationshipTermBase>
Concrete implementations of this abstract base class express a directed relationship between two
cdm entities (
IRelated ). |
class |
RelationshipTermBase<T extends RelationshipTermBase<T>> |
class |
SourcedEntityBase<SOURCE extends OriginalSourceBase<? extends SourcedEntityBase<SOURCE>>>
Abstract class for all objects that may have (multiple) sources
|
class |
VersionableEntity
The class keeps track of versions via a full linked list to different version objects, or a simple updated/updatedBy property in the same object.
|
Modifier and Type | Class and Description |
---|---|
class |
CategoricalData
This class represents information pieces expressed in categorical type of
data (in opposition to
quantitative data on one side and to literal data on
the other side). |
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 |
CommonTaxonName
This class represents common or vernacular names for
taxa . |
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 |
DescriptionElementBase
The upmost (abstract) class for a piece of information) about
a
specimen , a taxon or even a taxon name . |
class |
DescriptionElementSource
This class represents an
IOriginalSource
that can be used with description elements . |
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 |
Distribution
This class represents elementary distribution data for a
taxon . |
class |
Feature
The class for individual properties (also designed as character, type or
category) of observed phenomena able to be described or measured.
|
class |
FeatureState
A class representing a state for a given feature.
|
class |
IndividualsAssociation
This class represents associations between the described
specimen or observation
and a second one (for instance a host). |
class |
KeyStatement
This class represents a statement or a question within a (polytomous) key.
|
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 |
PolytomousKeyNode
This class represents a node within a
polytomous key
structure. |
class |
PresenceAbsenceTerm
|
class |
QuantitativeData
This class represents information pieces expressed in numerical data
(in opposition to
categorical data on one side and to literal data on
the other side). |
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 |
StateData
This class represents the assignment of values (
state terms ) to features
corresponding to categorical data . |
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 |
StatisticalMeasurementValue
This class represents the assignment of numerical values to
features
corresponding to quantitative data . |
class |
TaxonDescription
This class represents descriptions that delimit or circumscribe a real taxon.
|
class |
TaxonInteraction
This class represents interactions between the described
taxon
and a second one (for instance a parasite, a prey or a hybrid parent). |
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 |
TextData
This class represents information pieces expressed in one or several natural
languages (for the
feature "medical use" for instance). |
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 |
AudioFile |
class |
ExternalLink
Class that represents a link to any web resource.
|
class |
IdentifiableMediaEntity<S extends IIdentifiableEntityCacheStrategy<?>> |
class |
ImageFile |
class |
Media
A
media is any kind of media that represents a media object. |
class |
MediaRepresentation
A media representation is basically anything having a MIME Media Type.
|
class |
MediaRepresentationPart
A media representation part is a resource that can be referenced by an URI.
|
class |
MovieFile |
class |
Rights
Typically, rights information includes a statement about various property
rights associated with the resource, including intellectual property rights.
|
class |
RightsType |
Modifier and Type | Class and Description |
---|---|
class |
CdmMetaData |
Modifier and Type | Class and Description |
---|---|
class |
Amplification
The physical process of amplification (also called PCR) extracts and replicates parts of the DNA of
a given
DNA Sample . |
class |
AmplificationResult
The physical process of amplification (also called PCR) extracts and replicates parts of the DNA of
a given
DNA Sample . |
class |
Cloning
Cloning is a method used in
DNA amplification for multiplying the base
material. |
class |
DnaQuality
A DNA Quality describes the quality of a
SpecimenOrObservationType.DnaSample |
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.
|
class |
Primer
A primer is a (short) DNA Sequence used for replication and extraction
of DNA parts during e.g.
|
class |
Sequence
Alignment of multiple
single sequences to a consensus sequence. |
class |
SingleRead
Instances of this the
SingleRead class describe the process and the result of a single
sequence generation (read). |
class |
SingleReadAlignment |
Modifier and Type | Class and Description |
---|---|
class |
HomotypicalGroup
The homotypical group class represents a set of
taxon names associated
on the base of their typifications. |
class |
HybridRelationship
The class representing a hybrid relationship between one of the
parents
of a hybrid taxon name and the hybrid taxon name itself. |
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 |
NameRelationship
The class representing a relationship between two
taxon names according
to the nomenclatural code which governs both of them. |
class |
NameRelationshipType
The class representing the categories of
taxon name relationships between
two taxon names . |
class |
NameTypeDesignation
The class representing a typification of a
taxon name with a rank
above "species aggregate" by another taxon name.According to nomenclature a type of a genus name or of any subdivision of a genus can only be a species name. |
class |
NameTypeDesignationStatus
The terms in this class define the status of a
name type designation . |
class |
NomenclaturalStatus
The class representing the assignation of a nomenclatural status to a
taxon name . |
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 |
Registration
A registration represents a nomenclatural act, either a
taxon name
registration or a type registration. |
class |
SpecimenTypeDesignation
The class representing a typification of one or several
taxon names by a
specimen or a figure . |
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 |
TextualTypeDesignation
|
class |
TypeDesignationBase<T extends TypeDesignationStatusBase<T>>
The (abstract) class representing a typification of one or several
taxon names .All taxon names which have a rank "species aggregate" or lower
can only be typified by specimens (a specimen type designation ), but taxon
names with a higher rank might be typified by an other taxon name with
rank "species" or "genus" (a name type designation ). |
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 |
DerivationEvent |
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 |
DeterminationEvent |
class |
FieldUnit
In situ observation of a taxon in the field.
|
class |
GatheringEvent
The event when gathering a specimen or recording a field unit only
|
class |
MaterialOrMethodEvent
A material or method event handles data on materials or methods used for handling specimen or derived units
in general.
|
class |
MediaSpecimen
Instances of MediaSpecimen represent a specimen which IS a media (photo, drawing, ...).
|
class |
PreservationMethod
This class is a specialization of
MaterialOrMethodEvent which allows to
specifically store temperature and XXX which are common parameters for preparation. |
class |
SpecimenOrObservationBase<S extends IIdentifiableEntityCacheStrategy<?>>
type figures are observations with at least a figure object in media
|
Modifier and Type | Class and Description |
---|---|
class |
AuthorityBase
Base class for persistable authorities.
|
class |
CdmAuthority
CDM authority class.
|
class |
GrantedAuthorityImpl |
class |
Group |
class |
Role
Role class.
|
class |
User |
Modifier and Type | Class and Description |
---|---|
class |
CdmLinkSource
Class to link to other CdmBase objects within the context of
information sources . |
class |
OriginalSourceBase<T extends ISourceable>
Abstract base class for classes implementing
IOriginalSource . |
class |
Reference
The class for references (information sources).
|
Modifier and Type | Class and Description |
---|---|
class |
AlternativeTreeRoot |
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 |
TaxonNode |
class |
TaxonNodeAgentRelation
This class relates a TaxonNode (Taxon within it's given publication context)
to an agent (person or team) and defining a type for this relationship.
|
class |
TaxonRelationship
The class representing a relationship between two
("accepted/correct") taxa . |
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 |
Representation
workaround for enumerations
|
class |
TermBase |
class |
TermCollection<TERM extends DefinedTermBase,REL extends TermRelationBase> |
class |
TermGraph<T extends DefinedTermBase> |
class |
TermGraphBase<TERM extends DefinedTermBase,REL extends TermRelationBase> |
class |
TermNode<T extends DefinedTermBase>
The class for tree nodes within a
feature tree structure. |
class |
TermRelation<T extends DefinedTermBase>
Class which creates a relation between 2
defined terms . |
class |
TermRelationBase<TERM extends DefinedTermBase,REL extends TermRelationBase,GRAPH extends TermGraphBase>
Common base class for
TermNode and TermRelation . |
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 | Class and Description |
---|---|
class |
EntityConstraintViolation
An
EntityConstraintViolation represents a single error resulting from
the validation of an entity. |
class |
EntityValidation
An
EntityValidation models the result of validating one entity, that
is, the outcome of calling Validator.validate(Object, Class...) . |
Copyright © 2007-2020 EDIT. All Rights Reserved.