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

A

AdaptedCsvRepository - Class in org.molgenis.ontology.matching

AdaptedCsvRepository(String, CsvRepository) - Constructor for class org.molgenis.ontology.matching.AdaptedCsvRepository

addClass(OWLClass, OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

addEntityMeta(EntityMetaData) - Method in class org.molgenis.ontology.importer.repository.OntologyRepositoryCollection

addSynonymsProperties(Set<String>) - Method in class org.molgenis.ontology.utils.OntologyLoader

ALLOWED_IDENTIFIER - Static variable in class org.molgenis.ontology.matching.AdaptedCsvRepository

C

calculateRoc(String, Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

calculateROC(String) - Method in class org.molgenis.ontology.roc.MatchQualityRocService

canImport(File, RepositoryCollection) - Method in class org.molgenis.ontology.importer.OntologyImportService

close() - Method in class org.molgenis.ontology.matching.AdaptedCsvRepository

CODE_SYSTEM - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

COMBINED_SCORE - Static variable in class org.molgenis.ontology.matching.OntologyServiceImpl

count() - Method in class org.molgenis.ontology.utils.OntologyLoader

createClass(String, Set<OWLClass>) - Method in class org.molgenis.ontology.utils.OntologyLoader

createStemmedWordSet(String) - Method in class org.molgenis.ontology.roc.InformationContentService

D

DATA_CREATED - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

DEFAULT_MATCHING_IDENTIFIER - Static variable in class org.molgenis.ontology.matching.OntologyServiceImpl

DEFAULT_MATCHING_NAME_FIELD - Static variable in class org.molgenis.ontology.matching.OntologyServiceImpl

DEFAULT_MATCHING_SYNONYM_FIELD - Static variable in class org.molgenis.ontology.matching.OntologyServiceImpl

DEFAULT_SEPARATOR - Static variable in class org.molgenis.ontology.matching.OntologyServiceImpl

deleteResult(String) - Method in class org.molgenis.ontology.controller.OntologyServiceController

doImport(RepositoryCollection, DatabaseAction, String) - Method in class org.molgenis.ontology.importer.OntologyImportService

download(String, HttpServletResponse, Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

E

ElasticsearchIndexManagerController - Class in org.molgenis.data.elasticsearch.admin

Index manager plugin

ElasticsearchIndexManagerController() - Constructor for class org.molgenis.data.elasticsearch.admin.ElasticsearchIndexManagerController

ElasticsearchIndexManagerService - Interface in org.molgenis.data.elasticsearch.admin

ElasticsearchIndexManagerServiceImpl - Class in org.molgenis.data.elasticsearch.admin

Elasticsearch index manager service that handles authorization

ElasticsearchIndexManagerServiceImpl(DataService) - Constructor for class org.molgenis.data.elasticsearch.admin.ElasticsearchIndexManagerServiceImpl

ENTITY_NAME - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

ENTITY_NAME - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

equals(Object) - Method in class org.molgenis.ontology.beans.OntologyImpl

equals(Object) - Method in class org.molgenis.ontology.beans.OntologyTermImpl

equals(Object) - Method in class org.molgenis.ontology.roc.OntologyWord

extractOWLClassId(OWLEntity) - Method in class org.molgenis.ontology.utils.OntologyLoader

F

findOntologyTerms(String, String) - Method in interface org.molgenis.ontology.matching.OntologyService

findOntologyTerms(String, String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

G

getAllAnnotationAxiom(OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

getAllclasses() - Method in class org.molgenis.ontology.utils.OntologyLoader

getAllDatabaseIds(OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

getAllOntologies() - Method in class org.molgenis.ontology.controller.OntologyManagerController

getAllOntologies() - Method in interface org.molgenis.ontology.matching.OntologyService

getAllOntologies() - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getAllOntologyEntities() - Method in interface org.molgenis.ontology.matching.OntologyService

getAllOntologyEntities() - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getAllOntologyTermEntities(String) - Method in interface org.molgenis.ontology.matching.OntologyService

getAllOntologyTermEntities(String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getAllOntologyTerms(String) - Method in interface org.molgenis.ontology.matching.OntologyService

getAllOntologyTerms(String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getAssociatedClasses(OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

getCapabilities() - Method in class org.molgenis.ontology.matching.AdaptedCsvRepository

getChildClass(OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

getChildOntologyTermEntities(String, String) - Method in interface org.molgenis.ontology.matching.OntologyService

getChildOntologyTermEntities(String, String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getChildOntologyTerms(String, String) - Method in interface org.molgenis.ontology.matching.OntologyService

getChildOntologyTerms(String, String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getCurrentJob(String) - Method in class org.molgenis.ontology.matching.UploadProgress

getDatabaseIds(OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

getDefinition(OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

getDescription() - Method in interface org.molgenis.ontology.beans.Ontology

getDescription() - Method in class org.molgenis.ontology.beans.OntologyImpl

getDescription() - Method in interface org.molgenis.ontology.beans.OntologyTerm

getDescription() - Method in class org.molgenis.ontology.beans.OntologyTermImpl

getEntityAsMap(Iterable<? extends Entity>) - Static method in class org.molgenis.ontology.utils.OntologyServiceUtil

getEntityAsMap(Entity) - Static method in class org.molgenis.ontology.utils.OntologyServiceUtil

getEntityMetaData() - Method in class org.molgenis.ontology.matching.AdaptedCsvRepository

getEntityName() - Method in class org.molgenis.ontology.request.OntologyServiceRequest

getEntityNames() - Method in class org.molgenis.ontology.importer.repository.OntologyRepositoryCollection

getEntityPager() - Method in class org.molgenis.ontology.request.OntologyServiceRequest

getFilterQuery() - Method in class org.molgenis.ontology.request.OntologyServiceRequest

getHashToRetrieveClass() - Method in class org.molgenis.ontology.utils.OntologyLoader

getId(OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

getIndexedEntities() - Method in interface org.molgenis.data.elasticsearch.admin.ElasticsearchIndexManagerService

Returns all indexed entity meta data sorted by entity label

getIndexedEntities() - Method in class org.molgenis.data.elasticsearch.admin.ElasticsearchIndexManagerServiceImpl

getInputData() - Method in class org.molgenis.ontology.beans.OntologyServiceResult

getIri() - Method in interface org.molgenis.ontology.beans.Ontology

getIri() - Method in class org.molgenis.ontology.beans.OntologyImpl

getIRI() - Method in interface org.molgenis.ontology.beans.OntologyTerm

getIRI() - Method in class org.molgenis.ontology.beans.OntologyTermImpl

getLabel() - Method in interface org.molgenis.ontology.beans.Ontology

getLabel() - Method in class org.molgenis.ontology.beans.OntologyImpl

getLabel() - Method in interface org.molgenis.ontology.beans.OntologyTerm

getLabel() - Method in class org.molgenis.ontology.beans.OntologyTermImpl

getLabel(OWLEntity) - Method in class org.molgenis.ontology.utils.OntologyLoader

getMessage() - Method in class org.molgenis.ontology.beans.OntologyServiceResult

getMustChangeEntityName() - Method in class org.molgenis.ontology.importer.OntologyImportService

getName() - Method in class org.molgenis.ontology.importer.repository.OntologyRepositoryCollection

getName() - Method in class org.molgenis.ontology.matching.AdaptedCsvRepository

getNodePath() - Method in class org.molgenis.ontology.utils.OWLClassContainer

getOntology() - Method in interface org.molgenis.ontology.beans.OntologyTerm

getOntology() - Method in class org.molgenis.ontology.beans.OntologyTermImpl

getOntology(String) - Method in interface org.molgenis.ontology.matching.OntologyService

getOntology(String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getOntologyEntity(String) - Method in interface org.molgenis.ontology.matching.OntologyService

getOntologyEntity(String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getOntologyFilePath() - Method in class org.molgenis.ontology.utils.OntologyLoader

getOntologyIri() - Method in class org.molgenis.ontology.request.OntologyServiceRequest

getOntologyIri() - Method in class org.molgenis.ontology.roc.OntologyWord

getOntologyIRI() - Method in class org.molgenis.ontology.utils.OntologyLoader

getOntologyLabel() - Method in class org.molgenis.ontology.utils.OntologyLoader

getOntologyName() - Method in class org.molgenis.ontology.utils.OntologyLoader

getOntologyTerm(String, String) - Method in interface org.molgenis.ontology.matching.OntologyService

getOntologyTerm(String, String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getOntologyTermEntity(String, String) - Method in interface org.molgenis.ontology.matching.OntologyService

getOntologyTermEntity(String, String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getOntologyTerms() - Method in class org.molgenis.ontology.beans.OntologyServiceResult

getOntologyTermSynonyms(String, String) - Method in interface org.molgenis.ontology.matching.OntologyService

getOntologyTermSynonyms(String, String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getOrder() - Method in class org.molgenis.ontology.importer.OntologyImportService

getOwlClass() - Method in class org.molgenis.ontology.utils.OWLClassContainer

getPercentage(String) - Method in class org.molgenis.ontology.matching.UploadProgress

getRepository(String) - Method in class org.molgenis.ontology.importer.repository.OntologyRepositoryCollection

getRootClasses() - Method in class org.molgenis.ontology.utils.OntologyLoader

getRootOntologyTermEntities(String) - Method in interface org.molgenis.ontology.matching.OntologyService

getRootOntologyTermEntities(String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getRootOntologyTerms(String) - Method in interface org.molgenis.ontology.matching.OntologyService

getRootOntologyTerms(String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

getSearchResult() - Method in class org.molgenis.ontology.response.OntologyServiceBatchResponse

getSubClassAxiomsForSubClass(OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

getSubClassAxiomsForSuperClass(OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

getSupportedDatabaseActions() - Method in class org.molgenis.ontology.importer.OntologyImportService

getSupportedFileExtensions() - Method in class org.molgenis.ontology.importer.OntologyImportService

getSynonyms() - Method in interface org.molgenis.ontology.beans.OntologyTerm

getSynonyms() - Method in class org.molgenis.ontology.beans.OntologyTermImpl

getSynonyms(OWLClass) - Method in class org.molgenis.ontology.utils.OntologyLoader

getTerm() - Method in class org.molgenis.ontology.response.OntologyServiceBatchResponse

getTermAccession() - Method in interface org.molgenis.ontology.beans.OntologyTerm

getTermAccession() - Method in class org.molgenis.ontology.beans.OntologyTermImpl

getThreshold(String) - Method in class org.molgenis.ontology.matching.UploadProgress

getTopClass() - Method in class org.molgenis.ontology.utils.OntologyLoader

getTotalHitCount() - Method in class org.molgenis.ontology.beans.OntologyServiceResult

getUserClickMode(String) - Method in class org.molgenis.ontology.matching.UploadProgress

getVersion() - Method in interface org.molgenis.ontology.beans.Ontology

getVersion() - Method in class org.molgenis.ontology.beans.OntologyImpl

getWord() - Method in class org.molgenis.ontology.roc.OntologyWord

H

hashCode() - Method in class org.molgenis.ontology.beans.OntologyImpl

hashCode() - Method in class org.molgenis.ontology.beans.OntologyTermImpl

hashCode() - Method in class org.molgenis.ontology.roc.OntologyWord

hasRepository(String) - Method in class org.molgenis.ontology.importer.repository.OntologyRepositoryCollection

I

ID - Static variable in class org.molgenis.data.elasticsearch.admin.ElasticsearchIndexManagerController

ID - Static variable in class org.molgenis.ontology.controller.OntologyManagerController

ID - Static variable in class org.molgenis.ontology.controller.OntologyServiceController

ID - Static variable in class org.molgenis.ontology.tree.OntologyTreeController

IDENTIFIER - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

IDENTIFIER - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

incrementProgress(String) - Method in class org.molgenis.ontology.matching.UploadProgress

informationContentService() - Method in class org.molgenis.ontology.OntologyConfiguration

InformationContentService - Class in org.molgenis.ontology.roc

InformationContentService(DataService) - Constructor for class org.molgenis.ontology.roc.InformationContentService

init(Model) - Method in class org.molgenis.data.elasticsearch.admin.ElasticsearchIndexManagerController

init(Model) - Method in class org.molgenis.ontology.controller.OntologyManagerController

init(Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

init(Model) - Method in class org.molgenis.ontology.tree.OntologyTreeController

initialize() - Method in interface org.molgenis.ontology.initializer.OntologyScriptInitializer

initialize() - Method in class org.molgenis.ontology.initializer.OntologyScriptInitializerImpl

INPUT_TERM - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

INSTANCE - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

INSTANCE - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

integrationTestMetaData(MetaDataService, RepositoryCollection, String) - Method in class org.molgenis.ontology.importer.OntologyImportService

INVALID_TOTAL_NUMBER - Static variable in class org.molgenis.ontology.controller.OntologyServiceController

isMatched() - Method in class org.molgenis.ontology.request.OntologyServiceRequest

isRoot() - Method in class org.molgenis.ontology.utils.OWLClassContainer

isUserExists(String) - Method in class org.molgenis.ontology.matching.UploadProgress

iterator() - Method in class org.molgenis.ontology.importer.repository.OntologyRepositoryCollection

iterator() - Method in class org.molgenis.ontology.matching.AdaptedCsvRepository

L

loadOntology(String, File) - Method in class org.molgenis.ontology.utils.OntologyLoader

M

match(String, String, String, Model, HttpServletRequest) - Method in class org.molgenis.ontology.controller.OntologyServiceController

MATCHED_TERM - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

MatchingTaskContentEntityMetaData - Class in org.molgenis.ontology.matching

matchingTaskContentEntityMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

MatchingTaskEntityMetaData - Class in org.molgenis.ontology.matching

matchingTaskEntityMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

MatchInputTermBatchService - Class in org.molgenis.ontology.matching

MatchInputTermBatchService(DataService, UploadProgress, OntologyService) - Constructor for class org.molgenis.ontology.matching.MatchInputTermBatchService

matchQualityRocService() - Method in class org.molgenis.ontology.OntologyConfiguration

MatchQualityRocService - Class in org.molgenis.ontology.roc

MatchQualityRocService(DataService, OntologyService) - Constructor for class org.molgenis.ontology.roc.MatchQualityRocService

matchResult(String, Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

matchResult(OntologyServiceRequest, HttpServletRequest) - Method in class org.molgenis.ontology.controller.OntologyServiceController

matchResult(Map<String, Object>, HttpServletRequest) - Method in class org.molgenis.ontology.controller.OntologyServiceController

matchTask(Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

MOLGENIS_USER - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

O

onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.ontology.importer.OntologyImporterServiceRegistrator

Ontology - Interface in org.molgenis.ontology.beans

ONTOLOGY_MANAGER_PLUGIN - Static variable in class org.molgenis.ontology.controller.OntologyManagerController

OntologyConfiguration - Class in org.molgenis.ontology

OntologyConfiguration() - Constructor for class org.molgenis.ontology.OntologyConfiguration

OntologyDataConfig - Class in org.molgenis.ontology

OntologyDataConfig() - Constructor for class org.molgenis.ontology.OntologyDataConfig

OntologyImpl - Class in org.molgenis.ontology.beans

OntologyImpl(String, String, String) - Constructor for class org.molgenis.ontology.beans.OntologyImpl

OntologyImpl(Entity) - Constructor for class org.molgenis.ontology.beans.OntologyImpl

OntologyImporterServiceRegistrator - Class in org.molgenis.ontology.importer

OntologyImporterServiceRegistrator(OntologyImportService, ImportServiceFactory, OntologyScriptInitializer) - Constructor for class org.molgenis.ontology.importer.OntologyImporterServiceRegistrator

OntologyImportService - Class in org.molgenis.ontology.importer

OntologyImportService(FileRepositoryCollectionFactory, DataService, SearchService, PermissionSystemService) - Constructor for class org.molgenis.ontology.importer.OntologyImportService

OntologyLoader - Class in org.molgenis.ontology.utils

OntologyLoader(OWLOntologyManager, OWLDataFactory) - Constructor for class org.molgenis.ontology.utils.OntologyLoader

OntologyLoader(String, File) - Constructor for class org.molgenis.ontology.utils.OntologyLoader

OntologyManagerController - Class in org.molgenis.ontology.controller

OntologyManagerController() - Constructor for class org.molgenis.ontology.controller.OntologyManagerController

ontologyMatchingService() - Method in class org.molgenis.ontology.OntologyConfiguration

ontologyMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

OntologyRepositoryCollection - Class in org.molgenis.ontology.importer.repository

RepositoryCollection for the import of an owl file.

OntologyRepositoryCollection(File) - Constructor for class org.molgenis.ontology.importer.repository.OntologyRepositoryCollection

Creates a new OntologyRepositoryCollection for an ontology file

OntologyScriptInitializer - Interface in org.molgenis.ontology.initializer

OntologyScriptInitializerImpl - Class in org.molgenis.ontology.initializer

OntologyScriptInitializerImpl(DataService) - Constructor for class org.molgenis.ontology.initializer.OntologyScriptInitializerImpl

OntologyService - Interface in org.molgenis.ontology.matching

Makes Ontology trees manageable

OntologyServiceBatchResponse - Class in org.molgenis.ontology.response

OntologyServiceBatchResponse(String, SearchResult) - Constructor for class org.molgenis.ontology.response.OntologyServiceBatchResponse

OntologyServiceController - Class in org.molgenis.ontology.controller

OntologyServiceController() - Constructor for class org.molgenis.ontology.controller.OntologyServiceController

OntologyServiceImpl - Class in org.molgenis.ontology.matching

OntologyServiceImpl(DataService, SearchService, InformationContentService) - Constructor for class org.molgenis.ontology.matching.OntologyServiceImpl

OntologyServiceRequest - Class in org.molgenis.ontology.request

OntologyServiceRequest(String, String, String, boolean, EntityPager) - Constructor for class org.molgenis.ontology.request.OntologyServiceRequest

OntologyServiceResult - Class in org.molgenis.ontology.beans

This function is used to parse the results from OntologyService

OntologyServiceResult(String) - Constructor for class org.molgenis.ontology.beans.OntologyServiceResult

OntologyServiceResult(Map<String, Object>, Iterable<? extends Entity>, long) - Constructor for class org.molgenis.ontology.beans.OntologyServiceResult

OntologyServiceResult(Map<String, Object>, List<Map<String, Object>>, long) - Constructor for class org.molgenis.ontology.beans.OntologyServiceResult

OntologyServiceUtil - Class in org.molgenis.ontology.utils

OntologyServiceUtil() - Constructor for class org.molgenis.ontology.utils.OntologyServiceUtil

OntologyTerm - Interface in org.molgenis.ontology.beans

ontologyTermDynamicAnnotationMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

OntologyTermImpl - Class in org.molgenis.ontology.beans

OntologyTermImpl(String, String, String, String, Ontology) - Constructor for class org.molgenis.ontology.beans.OntologyTermImpl

OntologyTermImpl(Entity) - Constructor for class org.molgenis.ontology.beans.OntologyTermImpl

ontologyTermMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

ontologyTermNodePathMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

ontologyTermSynonymMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

OntologyTreeController - Class in org.molgenis.ontology.tree

OntologyTreeController() - Constructor for class org.molgenis.ontology.tree.OntologyTreeController

OntologyWord - Class in org.molgenis.ontology.roc

OntologyWord(String, String) - Constructor for class org.molgenis.ontology.roc.OntologyWord

org.molgenis.data.elasticsearch.admin - package org.molgenis.data.elasticsearch.admin

org.molgenis.ontology - package org.molgenis.ontology

org.molgenis.ontology.beans - package org.molgenis.ontology.beans

org.molgenis.ontology.controller - package org.molgenis.ontology.controller

org.molgenis.ontology.importer - package org.molgenis.ontology.importer

org.molgenis.ontology.importer.repository - package org.molgenis.ontology.importer.repository

org.molgenis.ontology.initializer - package org.molgenis.ontology.initializer

org.molgenis.ontology.matching - package org.molgenis.ontology.matching

org.molgenis.ontology.request - package org.molgenis.ontology.request

org.molgenis.ontology.response - package org.molgenis.ontology.response

org.molgenis.ontology.roc - package org.molgenis.ontology.roc

org.molgenis.ontology.tree - package org.molgenis.ontology.tree

org.molgenis.ontology.utils - package org.molgenis.ontology.utils

OWLClassContainer - Class in org.molgenis.ontology.utils

OWLClassContainer(OWLClass, String, boolean) - Constructor for class org.molgenis.ontology.utils.OWLClassContainer

P

preProcessing() - Method in class org.molgenis.ontology.utils.OntologyLoader

process(SecurityContext, MolgenisUser, String, Repository) - Method in class org.molgenis.ontology.matching.MatchInputTermBatchService

processInputTermService() - Method in class org.molgenis.ontology.OntologyConfiguration

R

rebuildIndex(String) - Method in interface org.molgenis.data.elasticsearch.admin.ElasticsearchIndexManagerService

Rebuilds the index for the given entity type

rebuildIndex(String) - Method in class org.molgenis.data.elasticsearch.admin.ElasticsearchIndexManagerServiceImpl

redistributedNGramScore(String, String) - Method in class org.molgenis.ontology.roc.InformationContentService

REF_ENTITY - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

registerOntologyRepositorySource() - Method in class org.molgenis.ontology.OntologyDataConfig

Registers the OntologyRepositorySource factory so it can be used by DataService.createFileRepositorySource(File file);

registerUser(String, String, Integer) - Method in class org.molgenis.ontology.matching.UploadProgress

registerUser(String, String) - Method in class org.molgenis.ontology.matching.UploadProgress

reindexType(ElasticsearchIndexManagerController.ReindexRequest) - Method in class org.molgenis.data.elasticsearch.admin.ElasticsearchIndexManagerController

removeIllegalCharWithEmptyString(String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

removeIllegalCharWithSingleWhiteSpace(String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

removeUser(String) - Method in class org.molgenis.ontology.matching.UploadProgress

resetUserThreshold(String, Integer) - Method in class org.molgenis.ontology.matching.UploadProgress

S

SCORE - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

SCORE - Static variable in class org.molgenis.ontology.matching.OntologyServiceImpl

search(Map<String, Object>, HttpServletRequest) - Method in class org.molgenis.ontology.controller.OntologyServiceController

search(String, String) - Method in interface org.molgenis.ontology.matching.OntologyService

search(String, String) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

searchEntity(String, Entity) - Method in interface org.molgenis.ontology.matching.OntologyService

searchEntity(String, Entity) - Method in class org.molgenis.ontology.matching.OntologyServiceImpl

setUserClickMode(String, Boolean) - Method in class org.molgenis.ontology.matching.UploadProgress

SIGNIFICANT_VALUE - Static variable in class org.molgenis.ontology.matching.OntologyServiceImpl

T

termFrequencyEntityMetaData() - Method in class org.molgenis.ontology.OntologyConfiguration

termFrequencyService() - Method in class org.molgenis.ontology.OntologyConfiguration

THRESHOLD - Static variable in class org.molgenis.ontology.matching.MatchingTaskEntityMetaData

toString() - Method in class org.molgenis.ontology.beans.OntologyImpl

toString() - Method in class org.molgenis.ontology.beans.OntologyTermImpl

U

unzip(File) - Static method in class org.molgenis.ontology.utils.ZipFileUtil

updateThreshold(String, String, Model) - Method in class org.molgenis.ontology.controller.OntologyServiceController

upload(String, String, Part, Model, HttpServletRequest) - Method in class org.molgenis.ontology.controller.OntologyServiceController

UploadProgress - Class in org.molgenis.ontology.matching

UploadProgress() - Constructor for class org.molgenis.ontology.matching.UploadProgress

uploadProgress() - Method in class org.molgenis.ontology.OntologyConfiguration

URI - Static variable in class org.molgenis.data.elasticsearch.admin.ElasticsearchIndexManagerController

URI - Static variable in class org.molgenis.ontology.controller.OntologyManagerController

URI - Static variable in class org.molgenis.ontology.controller.OntologyServiceController

URI - Static variable in class org.molgenis.ontology.tree.OntologyTreeController

V

VALIDATED - Static variable in class org.molgenis.ontology.matching.MatchingTaskContentEntityMetaData

validateImport(File, RepositoryCollection) - Method in class org.molgenis.ontology.importer.OntologyImportService

Z

ZipFileUtil - Class in org.molgenis.ontology.utils

ZipFileUtil() - Constructor for class org.molgenis.ontology.utils.ZipFileUtil

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