Index (worms-plugin 1.8.1-SNAPSHOT API)

A C D E F G H I L M N O P Q R S T U V W

A

aphiaAttributeKeysById(long, boolean) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get attribute definitions.
aphiaAttributesByAphiaId(long, boolean) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get a list of attributes for a given AphiaID
AphiaAttributeSets - Class in de.uni_jena.cs.fusion.client.worms
AphiaAttributeSets() - Constructor for class de.uni_jena.cs.fusion.client.worms.AphiaAttributeSets
aphiaAttributeValuesByCategoryId(long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get list values that are grouped by an CateogryID
aphiaChildrenByAphiaId(long, boolean) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get the direct children for a given AphiaID.
aphiaChildrenByAphiaId(long, boolean, long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get the direct children (max.
aphiaClassificationByAphiaId(long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get the complete classification for one taxon.
aphiaDistributionsByAphiaId(long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get all distributions for a given AphiaID External Identifiers
aphiaExternalIdByAphiaId(long, ExternalIdentifierSource) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get any external identifier(s) for a given AphiaID
aphiaId - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaAttributeSets: Unique and persistent identifier within WoRMS.
aphiaId - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: Unique and persistent identifier within WoRMS.
aphiaId - Variable in class de.uni_jena.cs.fusion.client.worms.Attribute: Unique and persistent identifier within WoRMS.
aphiaId - Variable in class de.uni_jena.cs.fusion.client.worms.Classification: Unique and persistent identifier within WoRMS.
aphiaIdByName(String) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get the AphiaID for a given name
aphiaIdInherited - Variable in class de.uni_jena.cs.fusion.client.worms.Attribute: The AphiaID from where this attribute is inherited
aphiaIdsByAttributeKeyId(long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get a list of AphiaIDs with attribute tree for a given attribute definition ID Distributions.
aphiaIdsByAttributeKeyId(long, long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get a list of AphiaIDs (max 50) with attribute tree for a given attribute definition ID Distributions.
aphiaNameByAphiaId(long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get the name for a given AphiaID
AphiaRecord - Class in de.uni_jena.cs.fusion.client.worms
AphiaRecord() - Constructor for class de.uni_jena.cs.fusion.client.worms.AphiaRecord
aphiaRecordByAphiaId(long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get the complete AphiaRecord for a given AphiaID
aphiaRecordByExternalId(String, ExternalIdentifierSource) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get the Aphia Record for a given external identifier Sources
aphiaRecordsByDate(TemporalAccessor, TemporalAccessor, boolean) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Lists all AphiaRecords (max.
aphiaRecordsByDate(TemporalAccessor, TemporalAccessor, boolean, long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Lists all AphiaRecords (max.
aphiaRecordsByMatchNames(List<String>, boolean) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: For each given scientific name (may include authority), try to find one or more AphiaRecords, using the TAXAMATCH fuzzy matching algorithm by Tony Rees.
aphiaRecordsByName(String, boolean, boolean) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get one or more matching AphiaRecords for a given name.
aphiaRecordsByName(String, boolean, boolean, long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get one or more matching AphiaRecords (max.
aphiaRecordsByNames(List<String>, boolean, boolean) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: For each given scientific name, try to find one or more AphiaRecords (max.
aphiaRecordsByVernacular(String, boolean) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get one or more Aphia Records for a given vernacular.
aphiaRecordsByVernacular(String, boolean, long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get one or more Aphia Records (max.
aphiaSourcesByAphiaId(long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get one or more sources/references including links, for one AphiaID
aphiaSynonymsByAphiaId(long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get all synonyms for a given AphiaID.
aphiaVernacularsByAphiaId(long) - Method in class de.uni_jena.cs.fusion.client.worms.WormsClient: Get all vernaculars for a given AphiaID
Attribute - Class in de.uni_jena.cs.fusion.client.worms
Attribute() - Constructor for class de.uni_jena.cs.fusion.client.worms.Attribute
AttributeKey - Class in de.uni_jena.cs.fusion.client.worms
AttributeKey() - Constructor for class de.uni_jena.cs.fusion.client.worms.AttributeKey
attributes - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaAttributeSets
AttributeValue - Class in de.uni_jena.cs.fusion.client.worms
AttributeValue() - Constructor for class de.uni_jena.cs.fusion.client.worms.AttributeValue
authority - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the authorship information for the scientific name formatted according to the conventions of the applicable nomenclaturalCode

C

categoryID - Variable in class de.uni_jena.cs.fusion.client.worms.Attribute: The category identifier to list possible attribute values for this attribute definition
categoryId - Variable in class de.uni_jena.cs.fusion.client.worms.AttributeKey: The category identifier to list possible attribute values for this attribute definition
child - Variable in class de.uni_jena.cs.fusion.client.worms.Classification
children - Variable in class de.uni_jena.cs.fusion.client.worms.Attribute: The possible child attributes that help to describe to current attribute
children - Variable in class de.uni_jena.cs.fusion.client.worms.AttributeKey: The possible child attribute keys that help to describe to current attribute
children - Variable in class de.uni_jena.cs.fusion.client.worms.AttributeValue: Child measurementValues that are more specific
citation - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: a bibliographic reference for the resource as a statement indicating how this record should be cited (attributed) when used
Classification - Class in de.uni_jena.cs.fusion.client.worms
Classification() - Constructor for class de.uni_jena.cs.fusion.client.worms.Classification
ClassificationCapabilityImpl - Class in org.gcube.data.spd.wormsplugin.capabilities
ClassificationCapabilityImpl() - Constructor for class org.gcube.data.spd.wormsplugin.capabilities.ClassificationCapabilityImpl
ClassificationCapabilityImpl.RecordType - Enum in org.gcube.data.spd.wormsplugin.capabilities
createCredits() - Static method in class org.gcube.data.spd.wormsplugin.Utils
createDate() - Static method in class org.gcube.data.spd.wormsplugin.Utils
credits - Static variable in class org.gcube.data.spd.wormsplugin.WormsPlugin

D

de.uni_jena.cs.fusion.client.worms - package de.uni_jena.cs.fusion.client.worms
decimalLatitude - Variable in class de.uni_jena.cs.fusion.client.worms.Distribution: The geographic latitude (in decimal degrees, WGS84)
decimalLongitude - Variable in class de.uni_jena.cs.fusion.client.worms.Distribution: The geographic longitude (in decimal degrees, WGS84)
Distribution - Class in de.uni_jena.cs.fusion.client.worms
Distribution() - Constructor for class de.uni_jena.cs.fusion.client.worms.Distribution
doi - Variable in class de.uni_jena.cs.fusion.client.worms.Source: Digital Object Identifier

E

establishmentMeans - Variable in class de.uni_jena.cs.fusion.client.worms.Distribution: The process by which the biological individual(s) represented in the Occurrence became established at the location.
ExpansionCapabilityImpl - Class in org.gcube.data.spd.wormsplugin.capabilities
ExpansionCapabilityImpl() - Constructor for class org.gcube.data.spd.wormsplugin.capabilities.ExpansionCapabilityImpl
ExternalIdentifierSource - Enum in de.uni_jena.cs.fusion.client.worms

F

fulltext - Variable in class de.uni_jena.cs.fusion.client.worms.Source: Full text link (PDF)

G

getClassificationInterface() - Method in class org.gcube.data.spd.wormsplugin.WormsPlugin
getDescription() - Method in class org.gcube.data.spd.wormsplugin.WormsPlugin
getExpansionInterface() - Method in class org.gcube.data.spd.wormsplugin.WormsPlugin
getMappingInterface() - Method in class org.gcube.data.spd.wormsplugin.WormsPlugin
getRelatedScientificNames(ObjectWriter<String>, String) - Method in class org.gcube.data.spd.wormsplugin.capabilities.NamesMappingImpl
getRepositoryInfo() - Method in class org.gcube.data.spd.wormsplugin.WormsPlugin
getRepositoryName() - Method in class org.gcube.data.spd.wormsplugin.WormsPlugin
getSupportedCapabilities() - Method in class org.gcube.data.spd.wormsplugin.WormsPlugin
getSupportedProperties() - Method in class org.gcube.data.spd.wormsplugin.capabilities.ClassificationCapabilityImpl
getSynonymnsById(ObjectWriter<TaxonomyItem>, String) - Method in class org.gcube.data.spd.wormsplugin.capabilities.ClassificationCapabilityImpl
getSynonyms(ObjectWriter<String>, String) - Method in class org.gcube.data.spd.wormsplugin.capabilities.ExpansionCapabilityImpl

H

higherGeography - Variable in class de.uni_jena.cs.fusion.client.worms.Distribution: A geographic name less specific than the information captured in the locality term.
higherGeographyID - Variable in class de.uni_jena.cs.fusion.client.worms.Distribution: An identifier for the geographic region within which the locality occurred, using MRGID

I

initialize(ServiceEndpoint) - Method in class org.gcube.data.spd.wormsplugin.WormsPlugin
inputId - Variable in class de.uni_jena.cs.fusion.client.worms.AttributeKey: The data type that is expected as value for this attribute definition
isBrackish - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: a boolean flag indicating whether the taxon occurrs in brackish habitats.
isExtinct - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: a flag indicating an extinct organism.
isFreshwater - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: a boolean flag indicating whether the taxon occurrs in freshwater habitats, i.e.
isMarine - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: a boolean flag indicating whether the taxon is a marine organism, i.e.
isTerrestrial - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: a boolean flag indicating the taxon is a terrestial organism, i.e.

L

language - Variable in class de.uni_jena.cs.fusion.client.worms.Vernacular
languageCode - Variable in class de.uni_jena.cs.fusion.client.worms.Vernacular
link - Variable in class de.uni_jena.cs.fusion.client.worms.Source: External link (i.e.
locality - Variable in class de.uni_jena.cs.fusion.client.worms.Distribution: The specific description of the place
locationID - Variable in class de.uni_jena.cs.fusion.client.worms.Distribution: An identifier for the locality.
lsid - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: LifeScience Identifier.

M

matchType - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: Type of match.
MatchType - Enum in de.uni_jena.cs.fusion.client.worms
measurementType - Variable in class de.uni_jena.cs.fusion.client.worms.Attribute: The corresponding AttributeKey its measurementType
measurementType - Variable in class de.uni_jena.cs.fusion.client.worms.AttributeKey: The nature of the measurement, fact, characteristic, or assertion http://www.marinespecies.org/traits/wiki
measurementTypeId - Variable in class de.uni_jena.cs.fusion.client.worms.Attribute: The corresponding AttributeKey its measurementTypeID
measurementTypeId - Variable in class de.uni_jena.cs.fusion.client.worms.AttributeKey: An internal identifier for the measurementType
measurementValue - Variable in class de.uni_jena.cs.fusion.client.worms.Attribute: The value of the measurement, fact, characteristic, or assertion
measurementValue - Variable in class de.uni_jena.cs.fusion.client.worms.AttributeValue: The value of the measurement, fact, characteristic, or assertion
measurementValueCode - Variable in class de.uni_jena.cs.fusion.client.worms.AttributeValue: Additional info/code that helps to the describe/define the measurementValue
measurementValueId - Variable in class de.uni_jena.cs.fusion.client.worms.AttributeValue: An identifier for facts stored in the column measurementValue
modified - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: The most recent date-time in GMT on which the resource was changed

N

NamesMappingImpl - Class in org.gcube.data.spd.wormsplugin.capabilities
NamesMappingImpl() - Constructor for class org.gcube.data.spd.wormsplugin.capabilities.NamesMappingImpl

O

org.gcube.data.spd.wormsplugin - package org.gcube.data.spd.wormsplugin
org.gcube.data.spd.wormsplugin.capabilities - package org.gcube.data.spd.wormsplugin.capabilities

P

page - Variable in class de.uni_jena.cs.fusion.client.worms.Source: Page(s) where the taxon is mentioned
parentNameUsageID - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord

Q

qualityStatus - Variable in class de.uni_jena.cs.fusion.client.worms.Attribute: Quality status of the record.
qualityStatus - Variable in class de.uni_jena.cs.fusion.client.worms.Distribution: Quality status of the record.

R

recordStatus - Variable in class de.uni_jena.cs.fusion.client.worms.Distribution: The status of the distribution record.
reference - Variable in class de.uni_jena.cs.fusion.client.worms.Attribute: The AphiaSource reference for this attribute
reference - Variable in class de.uni_jena.cs.fusion.client.worms.Source: Full citation string
retrieveTaxa(ObjectWriter<TaxonomyItem>, String, ClassificationCapabilityImpl.RecordType) - Method in class org.gcube.data.spd.wormsplugin.capabilities.ClassificationCapabilityImpl
retrieveTaxon(Classification, long) - Static method in class org.gcube.data.spd.wormsplugin.Utils
retrieveTaxonById(String) - Method in class org.gcube.data.spd.wormsplugin.capabilities.ClassificationCapabilityImpl
retrieveTaxonByIds(Iterator<String>, ClosableWriter<TaxonomyItem>) - Method in class org.gcube.data.spd.wormsplugin.capabilities.ClassificationCapabilityImpl
retrieveTaxonChildrenByTaxonId(String) - Method in class org.gcube.data.spd.wormsplugin.capabilities.ClassificationCapabilityImpl
retrieveTaxonomy(Classification, long) - Static method in class org.gcube.data.spd.wormsplugin.Utils

S

scientificName - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the full scientific name without authorship
scientificName - Variable in class de.uni_jena.cs.fusion.client.worms.Classification: the full scientific name without authorship
search(String, ObjectWriter<ResultItem>, String) - Method in class org.gcube.data.spd.wormsplugin.WormsPlugin
searchByScientificName(String, ObjectWriter<TaxonomyItem>, Condition...) - Method in class org.gcube.data.spd.wormsplugin.capabilities.ClassificationCapabilityImpl
searchByScientificName(String, ObjectWriter<ResultItem>, Condition...) - Method in class org.gcube.data.spd.wormsplugin.WormsPlugin
Source - Class in de.uni_jena.cs.fusion.client.worms
Source() - Constructor for class de.uni_jena.cs.fusion.client.worms.Source
sourceId - Variable in class de.uni_jena.cs.fusion.client.worms.Attribute: The identifier for the AphiaSource for this attribute
sourceId - Variable in class de.uni_jena.cs.fusion.client.worms.Source: Unique identifier for the source within WoRMS.
status - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the status of the use of the scientific name (usually a taxonomic opinion).

T

taxonomicClass - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the full scientific name of the class in which the taxon is classified
taxonomicFamily - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the full scientific name of the family in which the taxon is classified
taxonomicGenus - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the full scientific name of the genus in which the taxon is classified
taxonomicKingdom - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the full scientific name of the kingdom in which the taxon is classified
taxonomicOrder - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the full scientific name of the order in which the taxon is classified
taxonomicPhylum - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the full scientific name of the phylum or division in which the taxon is classified
taxonomicRank - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the taxonomic rank of the most specific name in the scientific name
taxonomicRank - Variable in class de.uni_jena.cs.fusion.client.worms.Classification: the taxonomic rank of the most specific name in the scientific name
taxonRankID - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord
typeStatus - Variable in class de.uni_jena.cs.fusion.client.worms.Distribution: The type status of the distribution.

U

unacceptReason - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the reason why a scientific name is unaccepted
url - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: HTTP URL to the AphiaRecord
url - Variable in class de.uni_jena.cs.fusion.client.worms.Source: Direct link to the source record
use - Variable in class de.uni_jena.cs.fusion.client.worms.Source: Usage of the source for this taxon.
Utils - Class in org.gcube.data.spd.wormsplugin
Utils() - Constructor for class org.gcube.data.spd.wormsplugin.Utils

V

validAphiaId - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the AphiaID (for the scientific name) of the currently accepted taxon.
validAuthority - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the authorship information for the scientific name of the currently accepted taxon
validName - Variable in class de.uni_jena.cs.fusion.client.worms.AphiaRecord: the scientific name of the currently accepted taxon
valueOf(String) - Static method in enum de.uni_jena.cs.fusion.client.worms.ExternalIdentifierSource: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.uni_jena.cs.fusion.client.worms.MatchType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum org.gcube.data.spd.wormsplugin.capabilities.ClassificationCapabilityImpl.RecordType: Returns the enum constant of this type with the specified name.
values() - Static method in enum de.uni_jena.cs.fusion.client.worms.ExternalIdentifierSource: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.uni_jena.cs.fusion.client.worms.MatchType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum org.gcube.data.spd.wormsplugin.capabilities.ClassificationCapabilityImpl.RecordType: Returns an array containing the constants of this enum type, in the order they are declared.
Vernacular - Class in de.uni_jena.cs.fusion.client.worms
Vernacular() - Constructor for class de.uni_jena.cs.fusion.client.worms.Vernacular
vernacular - Variable in class de.uni_jena.cs.fusion.client.worms.Vernacular

W

WormsClient - Class in de.uni_jena.cs.fusion.client.worms: A client for the World Register of Marine Species REST API.
WormsClient() - Constructor for class de.uni_jena.cs.fusion.client.worms.WormsClient: Constructs a WormsClient with a default CloseableHttpClient configured to a maximum number of 10 connections.
WormsClient(CloseableHttpClient) - Constructor for class de.uni_jena.cs.fusion.client.worms.WormsClient: Constructs a WormsClient using the specified CloseableHttpClient.
wormsClient - Static variable in class org.gcube.data.spd.wormsplugin.WormsPlugin
WormsClientException - Exception in de.uni_jena.cs.fusion.client.worms
WormsClientException() - Constructor for exception de.uni_jena.cs.fusion.client.worms.WormsClientException
WormsClientException(String) - Constructor for exception de.uni_jena.cs.fusion.client.worms.WormsClientException
WormsClientException(Throwable) - Constructor for exception de.uni_jena.cs.fusion.client.worms.WormsClientException
WormsClientException(String, Throwable) - Constructor for exception de.uni_jena.cs.fusion.client.worms.WormsClientException
WormsPlugin - Class in org.gcube.data.spd.wormsplugin
WormsPlugin() - Constructor for class org.gcube.data.spd.wormsplugin.WormsPlugin

A C D E F G H I L M N O P Q R S T U V W