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

A

AbstractOntologyEntity - Class in org.molgenis.omx.biobankconnect.ontologytree

AbstractOntologyEntity(Hit, EntityMetaData, SearchService) - Constructor for class org.molgenis.omx.biobankconnect.ontologytree.AbstractOntologyEntity

AbstractOntologyQueryRepository - Class in org.molgenis.omx.biobankconnect.ontology.repository

AbstractOntologyQueryRepository(String, SearchService) - Constructor for class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyQueryRepository

AbstractOntologyRepository - Class in org.molgenis.omx.biobankconnect.ontology.repository

AbstractOntologyRepository(String, SearchService) - Constructor for class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

addAnnotations(OWLClass, Set<OWLAnnotation>) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

addClass(OWLClass, OWLClass) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

addLabel(OWLClass, String) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

addSynonym(OWLClass, String) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

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

afterPropertiesSet() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

afterPropertiesSet() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

AlgorithmEditorController - Class in org.molgenis.omx.biobankconnect.algorithm

AlgorithmEditorController() - Constructor for class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

AlgorithmGenerateResponse - Class in org.molgenis.omx.biobankconnect.ontologymatcher

AlgorithmGenerateResponse(String, Boolean, Integer, Integer, Integer, List<Integer>, Integer) - Constructor for class org.molgenis.omx.biobankconnect.ontologymatcher.AlgorithmGenerateResponse

AlgorithmGenerator - Class in org.molgenis.omx.biobankconnect.algorithm

AlgorithmGenerator() - Constructor for class org.molgenis.omx.biobankconnect.algorithm.AlgorithmGenerator

algorithmGenerator() - Method in class org.molgenis.omx.biobankconnect.BiobankConnectConfig

AlgorithmReportPage - Class in org.molgenis.omx.biobankconnect.wizard

AlgorithmReportPage() - Constructor for class org.molgenis.omx.biobankconnect.wizard.AlgorithmReportPage

AlgorithmScriptLibrary - Class in org.molgenis.omx.biobankconnect.algorithm

AlgorithmScriptLibrary() - Constructor for class org.molgenis.omx.biobankconnect.algorithm.AlgorithmScriptLibrary

algorithmScriptLibrary() - Method in class org.molgenis.omx.biobankconnect.BiobankConnectConfig

AlgorithmUnitConverter - Class in org.molgenis.omx.biobankconnect.algorithm

AlgorithmUnitConverter() - Constructor for class org.molgenis.omx.biobankconnect.algorithm.AlgorithmUnitConverter

algorithmUnitConverter() - Method in class org.molgenis.omx.biobankconnect.BiobankConnectConfig

ALTERNATIVE_DEFINITION - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

annotate(Integer, List<String>) - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

annotate(Integer, List<String>) - Method in interface org.molgenis.omx.biobankconnect.ontologyannotator.OntologyAnnotator

annotate(HttpServletRequest) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

annotateDataItem(String, ObservableFeature, String, PorterStemmer) - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

applyAlgorithm(String, Integer, List<Integer>) - Method in class org.molgenis.omx.biobankconnect.algorithm.ApplyAlgorithms

ApplyAlgorithms - Class in org.molgenis.omx.biobankconnect.algorithm

ApplyAlgorithms() - Constructor for class org.molgenis.omx.biobankconnect.algorithm.ApplyAlgorithms

applyAlgorithms() - Method in class org.molgenis.omx.biobankconnect.BiobankConnectConfig

AsyncOntologyAnnotator - Class in org.molgenis.omx.biobankconnect.ontologyannotator

AsyncOntologyAnnotator() - Constructor for class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

AsyncOntologyIndexer - Class in org.molgenis.omx.biobankconnect.ontologyindexer

AsyncOntologyIndexer(SearchService, DataService) - Constructor for class org.molgenis.omx.biobankconnect.ontologyindexer.AsyncOntologyIndexer

AsyncOntologyMatcher - Class in org.molgenis.omx.biobankconnect.ontologymatcher

AsyncOntologyMatcher() - Constructor for class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

AsyncOntologyMatcher.OntologyTermContainer - Class in org.molgenis.omx.biobankconnect.ontologymatcher

AsyncOntologyMatcher.OntologyTermContainer(String) - Constructor for class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher.OntologyTermContainer

B

BiobankConnectConfig - Class in org.molgenis.omx.biobankconnect

BiobankConnectConfig() - Constructor for class org.molgenis.omx.biobankconnect.BiobankConnectConfig

BiobankConnectController - Class in org.molgenis.omx.biobankconnect.wizard

BiobankConnectController(ChooseCataloguePage, OntologyAnnotatorPage, OntologyMatcherPage, MappingManagerPage, AlgorithmReportPage) - Constructor for class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

BiobankConnectWizard - Class in org.molgenis.omx.biobankconnect.wizard

BiobankConnectWizard() - Constructor for class org.molgenis.omx.biobankconnect.wizard.BiobankConnectWizard

C

checkExistingMappings(String, DataService) - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

checkExistingMappings(String, DataService) - Method in interface org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcher

checkMatch() - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

CHIDLREN - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

ChooseCataloguePage - Class in org.molgenis.omx.biobankconnect.wizard

ChooseCataloguePage(DataService) - Constructor for class org.molgenis.omx.biobankconnect.wizard.ChooseCataloguePage

close() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

close() - Method in class org.molgenis.omx.biobankconnect.utils.StoreMappingRepository

collectCategoryInfo(RepositoryCollection) - Method in class org.molgenis.omx.biobankconnect.utils.OpalToOmxConvertor

collectCategoryInfo(RepositoryCollection) - Method in class org.molgenis.omx.biobankconnect.utils.PhenoToOmxConvertor

collectProtocolInfo(RepositoryCollection) - Method in class org.molgenis.omx.biobankconnect.utils.OpalToOmxConvertor

collectProtocolInfo(RepositoryCollection) - Method in class org.molgenis.omx.biobankconnect.utils.PhenoToOmxConvertor

collectVariableInfo(RepositoryCollection) - Method in class org.molgenis.omx.biobankconnect.utils.OpalToOmxConvertor

collectVariableInfo(RepositoryCollection) - Method in class org.molgenis.omx.biobankconnect.utils.PhenoToOmxConvertor

compareTo(TermComparison) - Method in class org.molgenis.omx.biobankconnect.utils.TermComparison

Concept - Class in org.molgenis.omx.biobankconnect.mesh

Concept() - Constructor for class org.molgenis.omx.biobankconnect.mesh.Concept

ConceptList - Class in org.molgenis.omx.biobankconnect.mesh

ConceptList() - Constructor for class org.molgenis.omx.biobankconnect.mesh.ConceptList

ConceptName - Class in org.molgenis.omx.biobankconnect.mesh

ConceptName() - Constructor for class org.molgenis.omx.biobankconnect.mesh.ConceptName

convert(OntologyTerm, OntologyTerm) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmUnitConverter

copyCategoryContent(AbstractOmxConvertor.UniqueCategory) - Method in class org.molgenis.omx.biobankconnect.utils.PhenoToOmxConvertor

copyClass(OWLClass, OWLClass, OntologyLoader) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

copyObject(ObservableFeature) - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

copyOntologyContent(Set<String>) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyManager

copySubclass(OWLClass, OntologyLoader) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

count() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyQueryRepository

count() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyIndexRepository

count(Query) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyQueryRepository

count() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermIndexRepository

count(Query) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermQueryRepository

createAnnotation(String, String) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

createDefinitionAnnotation(String) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

createDerivedDataSetIdentifier(String, String, List<Integer>) - Static method in class org.molgenis.omx.biobankconnect.algorithm.ApplyAlgorithms

createDerivedDataSetIdentifier(String, String, String) - Static method in class org.molgenis.omx.biobankconnect.algorithm.ApplyAlgorithms

createLabelAnnotation(String) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

createMappingDataSetIdentifier(String, Integer, Integer) - Static method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

createMappings(OntologyMatcherRequest) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

createOntology(String) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

createOntologyDocumentType(String) - Static method in class org.molgenis.omx.biobankconnect.ontologyindexer.AsyncOntologyIndexer

createOntologyTermDocumentType(String) - Static method in class org.molgenis.omx.biobankconnect.ontologyindexer.AsyncOntologyIndexer

createOWLClass(String) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

createValueFromAlgorithm(String, Integer, String) - Method in class org.molgenis.omx.biobankconnect.algorithm.ApplyAlgorithms

createWizard() - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

currentUserStatus() - Method in class org.molgenis.omx.biobankconnect.BiobankConnectConfig

CurrentUserStatus - Class in org.molgenis.omx.biobankconnect.wizard

CurrentUserStatus() - Constructor for class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

CurrentUserStatus.STAGE - Enum in org.molgenis.omx.biobankconnect.wizard

D

DateCreated - Class in org.molgenis.omx.biobankconnect.mesh

DateCreated() - Constructor for class org.molgenis.omx.biobankconnect.mesh.DateCreated

DEFAULT_ONTOLOGY_REPO - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyQueryRepository

DEFAULT_ONTOLOGY_TERM_REPO - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermQueryRepository

DEFAULT_SEPARATOR - Static variable in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyService

deleteDocumentByIds(String, List<String>) - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

deleteDocumentByIds(String, List<String>) - Method in interface org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcher

DescriptorName - Class in org.molgenis.omx.biobankconnect.mesh

DescriptorName() - Constructor for class org.molgenis.omx.biobankconnect.mesh.DescriptorName

DescriptorRecord - Class in org.molgenis.omx.biobankconnect.mesh

DescriptorRecord() - Constructor for class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

DescriptorRecordSet - Class in org.molgenis.omx.biobankconnect.mesh

DescriptorRecordSet() - Constructor for class org.molgenis.omx.biobankconnect.mesh.DescriptorRecordSet

download(HttpServletResponse, Model) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceController

download(String, HttpServletResponse) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

E

ENTITY_TYPE - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

entityMetaData - Variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

entityMetaData - Variable in class org.molgenis.omx.biobankconnect.ontologytree.AbstractOntologyEntity

entityName - Variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

equals(Object) - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher.OntologyTermContainer

extractFeatureName(String) - Static method in class org.molgenis.omx.biobankconnect.algorithm.ApplyAlgorithms

F

FIELDTYPE - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

findAll(Iterable<Object>) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyQueryRepository

findAll(Query, Class<E>) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyQueryRepository

findAll(Iterable<Object>, Class<E>) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyQueryRepository

findAll(Query) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyQueryRepository

findAll(Query) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermQueryRepository

findOne(Object, Class<E>) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyQueryRepository

findOne(Query, Class<E>) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyQueryRepository

findOne(Query) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyQueryRepository

findOne(Object) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyQueryRepository

findOne(Query) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermQueryRepository

findOne(Object) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermQueryRepository

findOneInternal(String, Query) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyQueryRepository

findOntologyTerm(List<String>) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmScriptLibrary

findOntologyTerm(String, String, String) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyService

findOntologyTermSynonyms(Hit) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmScriptLibrary

findScriptTemplate(ObservableFeature) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmScriptLibrary

finishedPercentage() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

finishedPercentage() - Method in interface org.molgenis.omx.biobankconnect.ontologyannotator.OntologyAnnotator

G

generateAlgorithm(String, OntologyMatcherRequest) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmGenerator

generateMapping(String, Integer, Integer, Integer) - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

This method is to generate a list of candidate mappings for the chosen feature by using ElasticSearch based on the information from ontology terms

generateMapping(String, Integer, Integer, Integer) - Method in interface org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcher

get(String) - Method in class org.molgenis.omx.biobankconnect.ontologytree.OntologyEntity

get(String) - Method in class org.molgenis.omx.biobankconnect.ontologytree.OntologyTermEntity

getAlgorithmScript() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcherRequest

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

getAllAttributes(Map<String, Object>) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

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

getAllOntologies() - Method in class org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexerController

getAllOntologies() - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyService

getAllPaths() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher.OntologyTermContainer

getAlternativeDefinitions() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher.OntologyTermContainer

getAnnotation() - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

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

getAttributeNames() - Method in class org.molgenis.omx.biobankconnect.ontologytree.AbstractOntologyEntity

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

getChildren(String, String, String) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyService

getConceptList() - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

getConceptName() - Method in class org.molgenis.omx.biobankconnect.mesh.Concept

getConcepts() - Method in class org.molgenis.omx.biobankconnect.mesh.ConceptList

getConceptUI() - Method in class org.molgenis.omx.biobankconnect.mesh.Concept

getCurrentUsers() - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

getDataSetId() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.UpdateIndexRequest

getDataSets() - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectWizard

getDataSetsForMappings(String) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

getDateCreated() - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

getDay() - Method in class org.molgenis.omx.biobankconnect.mesh.DateCreated

getDefinition() - Method in class org.molgenis.omx.biobankconnect.mesh.MeshTerm

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

getDerivedDataSetId() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AlgorithmGenerateResponse

getDescriptorName() - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

getDescriptorRecords() - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecordSet

getDescriptorUI() - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

getDocumentIds() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.UpdateIndexRequest

getDocumentType() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.UpdateIndexRequest

getDynamaticFields() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermIndexRepository

getEntityMetaData() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

getEntityMetaData() - Method in class org.molgenis.omx.biobankconnect.ontologytree.AbstractOntologyEntity

getEntityMetaData() - Method in class org.molgenis.omx.biobankconnect.utils.StoreMappingRepository

getFeatureId() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcherRequest

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

getHit() - Method in class org.molgenis.omx.biobankconnect.utils.TermComparison

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

getIdValue() - Method in class org.molgenis.omx.biobankconnect.ontologytree.AbstractOntologyEntity

getLabel() - Method in class org.molgenis.omx.biobankconnect.mesh.MeshTerm

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

getLabelAttributeNames() - Method in class org.molgenis.omx.biobankconnect.ontologytree.AbstractOntologyEntity

getMappedFeatureIds() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcherRequest

getMappings(Map<String, Object>) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

getMatchedDataSetIds() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.UpdateIndexRequest

getMatchePercentage() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AlgorithmGenerateResponse

getMonth() - Method in class org.molgenis.omx.biobankconnect.mesh.DateCreated

getName() - Method in class org.molgenis.omx.biobankconnect.mesh.ConceptName

getName() - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorName

getName() - Method in class org.molgenis.omx.biobankconnect.mesh.Term

getName() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

getOneAttribute(String) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

getOntologyByIri(String) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyService

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

getOntologyIRI() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher.OntologyTermContainer

getOntologyIri() - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceRequest

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

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

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

getOntologyUri() - Method in class org.molgenis.omx.biobankconnect.ontologyindexer.AsyncOntologyIndexer

getOntologyUri() - Method in interface org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexer

getOrder() - Method in class org.molgenis.omx.biobankconnect.ontologytree.OntologyRepositoryRegistrator

getPath() - Method in class org.molgenis.omx.biobankconnect.mesh.MeshTerm

getPercentageOfProcessForUser(String) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

getQueryField() - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceRequest

getQueryString() - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceRequest

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

getRootOntologyTerms(String) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyService

getScopeNote() - Method in class org.molgenis.omx.biobankconnect.mesh.Concept

getSearchResult() - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceBatchResponse

getSelectedBiobanks() - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectWizard

getSelectedDataSet() - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectWizard

getSelectedDataSetIds() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcherRequest

getSelectedDataSets() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AlgorithmGenerateResponse

getSelectedOntologyTerms() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher.OntologyTermContainer

getStage() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AlgorithmGenerateResponse

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

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

getSynonyms() - Method in class org.molgenis.omx.biobankconnect.mesh.MeshTerm

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

getTargetDataSet() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AlgorithmGenerateResponse

getTargetDataSetId() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcherRequest

getTerm() - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceBatchResponse

getTermList() - Method in class org.molgenis.omx.biobankconnect.mesh.Concept

getTerms() - Method in class org.molgenis.omx.biobankconnect.mesh.TermList

getTermUI() - Method in class org.molgenis.omx.biobankconnect.mesh.Term

getTitle() - Method in class org.molgenis.omx.biobankconnect.wizard.AlgorithmReportPage

getTitle() - Method in class org.molgenis.omx.biobankconnect.wizard.ChooseCataloguePage

getTitle() - Method in class org.molgenis.omx.biobankconnect.wizard.MappingManagerPage

getTitle() - Method in class org.molgenis.omx.biobankconnect.wizard.OntologyAnnotatorPage

getTitle() - Method in class org.molgenis.omx.biobankconnect.wizard.OntologyMatcherPage

getTopNode() - Method in class org.molgenis.omx.biobankconnect.mesh.MeshLoader

getTotalNumberOfUsers() - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

getTotalUsers() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AlgorithmGenerateResponse

getTreeNumberList() - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

getTreeNumbers() - Method in class org.molgenis.omx.biobankconnect.mesh.TreeNumberList

getUpdateScript() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.UpdateIndexRequest

getUrl() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

getUrl() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyIndexRepository

getUrl() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyQueryRepository

getUrl() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermIndexRepository

getUrl() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermQueryRepository

getUserCurrentStage(String) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

getUserName() - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectWizard

getYear() - Method in class org.molgenis.omx.biobankconnect.mesh.DateCreated

H

handleRequest(HttpServletRequest, BindingResult, Wizard) - Method in class org.molgenis.omx.biobankconnect.wizard.AlgorithmReportPage

handleRequest(HttpServletRequest, BindingResult, Wizard) - Method in class org.molgenis.omx.biobankconnect.wizard.ChooseCataloguePage

handleRequest(HttpServletRequest, BindingResult, Wizard) - Method in class org.molgenis.omx.biobankconnect.wizard.MappingManagerPage

handleRequest(HttpServletRequest, BindingResult, Wizard) - Method in class org.molgenis.omx.biobankconnect.wizard.OntologyAnnotatorPage

handleRequest(HttpServletRequest, BindingResult, Wizard) - Method in class org.molgenis.omx.biobankconnect.wizard.OntologyMatcherPage

harmonizationIndexer() - Method in class org.molgenis.omx.biobankconnect.BiobankConnectConfig

Get a reference to a HarmonizationIndexer.

hashCode() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher.OntologyTermContainer

hit - Variable in class org.molgenis.omx.biobankconnect.ontologytree.AbstractOntologyEntity

I

ID - Static variable in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

ID - Static variable in class org.molgenis.omx.biobankconnect.mappingmanager.MappingManagerController

ID - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

ID - Static variable in class org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexerController

ID - Static variable in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceController

ID - Static variable in class org.molgenis.omx.biobankconnect.ontologytree.OntologyTreeController

ID - Static variable in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

ILLEGAL_CHARACTERS_PATTERN - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

ILLEGAL_CHARACTERS_REPLACEMENT - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

importFeatures(String, Part, BiobankConnectWizard, HttpServletRequest, Model) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

incrementFinishedNumbers(String, int) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

incrementFinishedNumbersByOne(String) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

index(OntologyLoader) - Method in class org.molgenis.omx.biobankconnect.ontologyindexer.AsyncOntologyIndexer

index(OntologyLoader) - Method in interface org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexer

indexOntology(String, Part, Model) - Method in class org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexerController

init(String, HttpServletRequest, Model) - Method in class org.molgenis.omx.biobankconnect.mappingmanager.MappingManagerController

init(Model) - Method in class org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexerController

init(Model) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceController

init(Model) - Method in class org.molgenis.omx.biobankconnect.ontologytree.OntologyTreeController

initComplete() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

initComplete() - Method in interface org.molgenis.omx.biobankconnect.ontologyannotator.OntologyAnnotator

isComplete() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

isComplete() - Method in interface org.molgenis.omx.biobankconnect.ontologyannotator.OntologyAnnotator

isCorrectOntology() - Method in class org.molgenis.omx.biobankconnect.ontologyindexer.AsyncOntologyIndexer

isCorrectOntology() - Method in interface org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexer

isIndexingRunning() - Method in class org.molgenis.omx.biobankconnect.ontologyindexer.AsyncOntologyIndexer

isIndexingRunning() - Method in interface org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexer

isRunning() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

isRunning() - Method in interface org.molgenis.omx.biobankconnect.ontologyannotator.OntologyAnnotator

isRunning() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AlgorithmGenerateResponse

isRunning() - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

isRunning() - Method in interface org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcher

isRunning(HttpServletRequest) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

isUserLoggedIn(String, String) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

isUserMatching(String) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

iterator() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyQueryRepository

iterator(Class<E>) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyQueryRepository

iterator(Class<E>) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

iterator() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyIndexRepository

iterator(Class<E>) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyIndexRepository

iterator() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermIndexRepository

iterator(Class<E>) - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermIndexRepository

iterator() - Method in class org.molgenis.omx.biobankconnect.utils.StoreMappingRepository

L

LAST - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

loadExistingOntology(File) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyManager

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

M

main(String[]) - Static method in class org.molgenis.omx.biobankconnect.mesh.MeshLoaderApp

main(String[]) - Static method in class org.molgenis.omx.biobankconnect.utils.OntologyLoaderApp

main(String[]) - Static method in class org.molgenis.omx.biobankconnect.utils.OpalToOmxConvertor

main(String[]) - Static method in class org.molgenis.omx.biobankconnect.utils.PhenoToOmxConvertor

MappingManagerController - Class in org.molgenis.omx.biobankconnect.mappingmanager

MappingManagerController(OntologyMatcher, UserAccountService, DataService) - Constructor for class org.molgenis.omx.biobankconnect.mappingmanager.MappingManagerController

MappingManagerPage - Class in org.molgenis.omx.biobankconnect.wizard

MappingManagerPage() - Constructor for class org.molgenis.omx.biobankconnect.wizard.MappingManagerPage

match(String, Integer, List<Integer>, Integer) - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

match(String, Integer, List<Integer>, Integer) - Method in interface org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcher

match(String, String, Model) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceController

matchPercentage(String) - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

matchPercentage(String) - Method in interface org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcher

matchResult(EntityPager) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceController

MeshLoader - Class in org.molgenis.omx.biobankconnect.mesh

MeshLoader(File) - Constructor for class org.molgenis.omx.biobankconnect.mesh.MeshLoader

MeshLoaderApp - Class in org.molgenis.omx.biobankconnect.mesh

MeshLoaderApp() - Constructor for class org.molgenis.omx.biobankconnect.mesh.MeshLoaderApp

MeshTerm - Class in org.molgenis.omx.biobankconnect.mesh

MeshTerm(String, String, MeshTerm) - Constructor for class org.molgenis.omx.biobankconnect.mesh.MeshTerm

MeshTerm(String, MeshTerm) - Constructor for class org.molgenis.omx.biobankconnect.mesh.MeshTerm

MULTI_WHITESPACES - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

N

NGramMatchingModel - Class in org.molgenis.omx.biobankconnect.utils

This class has implemented Levenshtein distance algorithm so a similarity score could be calculated between two sequences.

NGramMatchingModel() - Constructor for class org.molgenis.omx.biobankconnect.utils.NGramMatchingModel

NODE_PATH - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

NODE_PATH_REPLACEMENT_PATTERN - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

O

onApplicationEvent(ContextRefreshedEvent) - Method in class org.molgenis.omx.biobankconnect.ontologytree.OntologyRepositoryRegistrator

onInit(HttpServletRequest) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

ONTOLOGY_IRI - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

ONTOLOGY_NAME - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

ONTOLOGY_TERM - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

ONTOLOGY_TERM_DEFINITION - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

ONTOLOGY_TERM_IRI - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

ontologyAnnotator() - Method in class org.molgenis.omx.biobankconnect.BiobankConnectConfig

OntologyAnnotator - Interface in org.molgenis.omx.biobankconnect.ontologyannotator

OntologyAnnotatorPage - Class in org.molgenis.omx.biobankconnect.wizard

OntologyAnnotatorPage() - Constructor for class org.molgenis.omx.biobankconnect.wizard.OntologyAnnotatorPage

OntologyCreator - Class in org.molgenis.omx.biobankconnect.utils

OntologyCreator(String) - Constructor for class org.molgenis.omx.biobankconnect.utils.OntologyCreator

OntologyCreator(OWLOntologyManager, OWLDataFactory, OntologyLoader) - Constructor for class org.molgenis.omx.biobankconnect.utils.OntologyCreator

OntologyEntity - Class in org.molgenis.omx.biobankconnect.ontologytree

OntologyEntity(Hit, EntityMetaData, OntologyService, SearchService) - Constructor for class org.molgenis.omx.biobankconnect.ontologytree.OntologyEntity

OntologyIndexer - Interface in org.molgenis.omx.biobankconnect.ontologyindexer

OntologyIndexerController - Class in org.molgenis.omx.biobankconnect.ontologyindexer

OntologyIndexerController() - Constructor for class org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexerController

OntologyIndexRepository - Class in org.molgenis.omx.biobankconnect.ontology.repository

OntologyIndexRepository(OntologyLoader, String, SearchService) - Constructor for class org.molgenis.omx.biobankconnect.ontology.repository.OntologyIndexRepository

OntologyLoader - Class in org.molgenis.omx.biobankconnect.utils

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

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

OntologyLoaderApp - Class in org.molgenis.omx.biobankconnect.utils

OntologyLoaderApp() - Constructor for class org.molgenis.omx.biobankconnect.utils.OntologyLoaderApp

OntologyManager - Class in org.molgenis.omx.biobankconnect.utils

OntologyManager() - Constructor for class org.molgenis.omx.biobankconnect.utils.OntologyManager

ontologyMatcher() - Method in class org.molgenis.omx.biobankconnect.BiobankConnectConfig

OntologyMatcher - Interface in org.molgenis.omx.biobankconnect.ontologymatcher

OntologyMatcherPage - Class in org.molgenis.omx.biobankconnect.wizard

OntologyMatcherPage() - Constructor for class org.molgenis.omx.biobankconnect.wizard.OntologyMatcherPage

OntologyMatcherRequest - Class in org.molgenis.omx.biobankconnect.ontologymatcher

OntologyMatcherRequest(Integer, Integer, List<Integer>, List<Integer>, String) - Constructor for class org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcherRequest

OntologyQueryRepository - Class in org.molgenis.omx.biobankconnect.ontology.repository

OntologyQueryRepository(String, OntologyService, SearchService) - Constructor for class org.molgenis.omx.biobankconnect.ontology.repository.OntologyQueryRepository

OntologyRepositoryRegistrator - Class in org.molgenis.omx.biobankconnect.ontologytree

OntologyRepositoryRegistrator(SearchService, DataService, OntologyService) - Constructor for class org.molgenis.omx.biobankconnect.ontologytree.OntologyRepositoryRegistrator

ontologyService() - Method in class org.molgenis.omx.biobankconnect.BiobankConnectConfig

OntologyService - Class in org.molgenis.omx.biobankconnect.ontologyservice

OntologyService(SearchService) - Constructor for class org.molgenis.omx.biobankconnect.ontologyservice.OntologyService

OntologyServiceBatchResponse - Class in org.molgenis.omx.biobankconnect.ontologyservice

OntologyServiceBatchResponse(String, SearchResult) - Constructor for class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceBatchResponse

OntologyServiceController - Class in org.molgenis.omx.biobankconnect.ontologyservice

OntologyServiceController() - Constructor for class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceController

OntologyServiceRequest - Class in org.molgenis.omx.biobankconnect.ontologyservice

OntologyServiceRequest(String, String, String) - Constructor for class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceRequest

OntologyTermEntity - Class in org.molgenis.omx.biobankconnect.ontologytree

OntologyTermEntity(Hit, EntityMetaData, SearchService) - Constructor for class org.molgenis.omx.biobankconnect.ontologytree.OntologyTermEntity

OntologyTermIndexRepository - Class in org.molgenis.omx.biobankconnect.ontology.repository

OntologyTermIndexRepository(OntologyLoader, String, SearchService) - Constructor for class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermIndexRepository

OntologyTermQueryRepository - Class in org.molgenis.omx.biobankconnect.ontology.repository

OntologyTermQueryRepository(String, String, SearchService) - Constructor for class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermQueryRepository

OntologyTreeController - Class in org.molgenis.omx.biobankconnect.ontologytree

OntologyTreeController() - Constructor for class org.molgenis.omx.biobankconnect.ontologytree.OntologyTreeController

OpalToOmxConvertor - Class in org.molgenis.omx.biobankconnect.utils

OpalToOmxConvertor(String, String) - Constructor for class org.molgenis.omx.biobankconnect.utils.OpalToOmxConvertor

org.molgenis.omx.biobankconnect - package org.molgenis.omx.biobankconnect

org.molgenis.omx.biobankconnect.algorithm - package org.molgenis.omx.biobankconnect.algorithm

org.molgenis.omx.biobankconnect.applicationevent - package org.molgenis.omx.biobankconnect.applicationevent

org.molgenis.omx.biobankconnect.mappingmanager - package org.molgenis.omx.biobankconnect.mappingmanager

org.molgenis.omx.biobankconnect.mesh - package org.molgenis.omx.biobankconnect.mesh

org.molgenis.omx.biobankconnect.ontology.repository - package org.molgenis.omx.biobankconnect.ontology.repository

org.molgenis.omx.biobankconnect.ontologyannotator - package org.molgenis.omx.biobankconnect.ontologyannotator

org.molgenis.omx.biobankconnect.ontologyindexer - package org.molgenis.omx.biobankconnect.ontologyindexer

org.molgenis.omx.biobankconnect.ontologymatcher - package org.molgenis.omx.biobankconnect.ontologymatcher

org.molgenis.omx.biobankconnect.ontologyservice - package org.molgenis.omx.biobankconnect.ontologyservice

org.molgenis.omx.biobankconnect.ontologytree - package org.molgenis.omx.biobankconnect.ontologytree

org.molgenis.omx.biobankconnect.utils - package org.molgenis.omx.biobankconnect.utils

org.molgenis.omx.biobankconnect.wizard - package org.molgenis.omx.biobankconnect.wizard

P

PARENT_NODE_PATH - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

PARENT_ONTOLOGY_TERM_IRI - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

parseOntologyTerms(Set<String>, OntologyLoader) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

PhenoToOmxConvertor - Class in org.molgenis.omx.biobankconnect.utils

PhenoToOmxConvertor(String, String) - Constructor for class org.molgenis.omx.biobankconnect.utils.PhenoToOmxConvertor

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

PROTOCOL_IDENTIFIER - Static variable in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

Q

query(OntologyServiceRequest) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

query() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyQueryRepository

query() - Method in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyTermQueryRepository

query(OntologyServiceRequest) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceController

R

recursiveVisit(MeshTerm, OntologyCreator) - Static method in class org.molgenis.omx.biobankconnect.mesh.MeshLoaderApp

rematch(OntologyMatcherRequest) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

removeAnnotations(Integer) - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

removeAnnotations(Integer) - Method in interface org.molgenis.omx.biobankconnect.ontologyannotator.OntologyAnnotator

removeAnnotations(HttpServletRequest) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

removeCurrentUserBySessionId(String) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

removeOntology(String) - Method in class org.molgenis.omx.biobankconnect.ontologyindexer.AsyncOntologyIndexer

removeOntology(String) - Method in interface org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexer

removeOntology(String, Model) - Method in class org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexerController

ROOT - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

S

saveOntology(File) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyCreator

saveOntology(File) - Method in class org.molgenis.omx.biobankconnect.utils.OntologyManager

saveScript(OntologyMatcherRequest) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

search(String, String) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyService

searchAllOntologies() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

searchService - Variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

searchService - Variable in class org.molgenis.omx.biobankconnect.ontologytree.AbstractOntologyEntity

sessionCreated(HttpSessionEvent) - Method in class org.molgenis.omx.biobankconnect.applicationevent.SessionExpireListener

sessionDestroyed(HttpSessionEvent) - Method in class org.molgenis.omx.biobankconnect.applicationevent.SessionExpireListener

SessionExpireListener - Class in org.molgenis.omx.biobankconnect.applicationevent

SessionExpireListener() - Constructor for class org.molgenis.omx.biobankconnect.applicationevent.SessionExpireListener

set(String, Object) - Method in class org.molgenis.omx.biobankconnect.ontologytree.AbstractOntologyEntity

set(Entity, boolean) - Method in class org.molgenis.omx.biobankconnect.ontologytree.AbstractOntologyEntity

setAnnotation(String) - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

setConceptList(ConceptList) - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

setConceptName(ConceptName) - Method in class org.molgenis.omx.biobankconnect.mesh.Concept

setConcepts(List<Concept>) - Method in class org.molgenis.omx.biobankconnect.mesh.ConceptList

setConceptUI(String) - Method in class org.molgenis.omx.biobankconnect.mesh.Concept

setDataSets(List<DataSet>) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectWizard

setDateCreated(DateCreated) - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

setDay(Integer) - Method in class org.molgenis.omx.biobankconnect.mesh.DateCreated

setDefinition(String) - Method in class org.molgenis.omx.biobankconnect.mesh.MeshTerm

setDescriptorName(DescriptorName) - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

setDescriptorRecords(List<DescriptorRecord>) - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecordSet

setDescriptorUI(String) - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

setLabel(String) - Method in class org.molgenis.omx.biobankconnect.mesh.MeshTerm

setMonth(Integer) - Method in class org.molgenis.omx.biobankconnect.mesh.DateCreated

setName(String) - Method in class org.molgenis.omx.biobankconnect.mesh.ConceptName

setName(String) - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorName

setName(String) - Method in class org.molgenis.omx.biobankconnect.mesh.Term

setScopeNote(String) - Method in class org.molgenis.omx.biobankconnect.mesh.Concept

setSearchService(SearchService) - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

setSearchService(SearchService) - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

setSelectedBiobanks(List<Integer>) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectWizard

setSelectedDataSet(DataSet) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectWizard

setSynonyms(Set<String>) - Method in class org.molgenis.omx.biobankconnect.mesh.MeshTerm

setTermList(TermList) - Method in class org.molgenis.omx.biobankconnect.mesh.Concept

setTerms(List<Term>) - Method in class org.molgenis.omx.biobankconnect.mesh.TermList

setTermUI(String) - Method in class org.molgenis.omx.biobankconnect.mesh.Term

setTreeNumberList(TreeNumberList) - Method in class org.molgenis.omx.biobankconnect.mesh.DescriptorRecord

setTreeNumbers(List<String>) - Method in class org.molgenis.omx.biobankconnect.mesh.TreeNumberList

setUserCurrentStage(String, CurrentUserStatus.STAGE) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

setUserIsRunning(String, Boolean) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

setUserLoggedIn(String, String) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

setUserName(String) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectWizard

setUserTotalNumberOfQueries(String, Long) - Method in class org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus

setYear(Integer) - Method in class org.molgenis.omx.biobankconnect.mesh.DateCreated

SINGLE_WHITESPACE - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

STOPWORDSLIST - Static variable in class org.molgenis.omx.biobankconnect.utils.NGramMatchingModel

STORE_MAPPING_ALGORITHM_SCRIPT - Static variable in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

STORE_MAPPING_CONFIRM_MAPPING - Static variable in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

STORE_MAPPING_FEATURE - Static variable in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

STORE_MAPPING_MAPPED_FEATURE - Static variable in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

STORE_MAPPING_SCORE - Static variable in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

StoreMappingRepository - Class in org.molgenis.omx.biobankconnect.utils

StoreMappingRepository(DataSet, DataService) - Constructor for class org.molgenis.omx.biobankconnect.utils.StoreMappingRepository

StoreMappingRepository(DataSet, List<ObservedValue>, DataService) - Constructor for class org.molgenis.omx.biobankconnect.utils.StoreMappingRepository

stringMatching(String, String) - Static method in class org.molgenis.omx.biobankconnect.utils.NGramMatchingModel

stringMatching(String, String, boolean) - Static method in class org.molgenis.omx.biobankconnect.utils.NGramMatchingModel

suggestScript(OntologyMatcherRequest) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

SYNONYMS - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

T

Term - Class in org.molgenis.omx.biobankconnect.mesh

Term() - Constructor for class org.molgenis.omx.biobankconnect.mesh.Term

TermComparison - Class in org.molgenis.omx.biobankconnect.utils

TermComparison(Hit) - Constructor for class org.molgenis.omx.biobankconnect.utils.TermComparison

TermList - Class in org.molgenis.omx.biobankconnect.mesh

TermList() - Constructor for class org.molgenis.omx.biobankconnect.mesh.TermList

testScrpit(OntologyMatcherRequest) - Method in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

toNestedQuery(List<QueryRule>) - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

toString() - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.UpdateIndexRequest

TreeNumberList - Class in org.molgenis.omx.biobankconnect.mesh

TreeNumberList() - Constructor for class org.molgenis.omx.biobankconnect.mesh.TreeNumberList

TYPE_ONTOLOGY - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.OntologyIndexRepository

TYPE_ONTOLOGYTERM - Static variable in class org.molgenis.omx.biobankconnect.ontology.repository.AbstractOntologyRepository

U

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

updateDocument(UpdateIndexRequest) - Method in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

updateIndex(UpdateIndexRequest) - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

updateIndex(UpdateIndexRequest) - Method in interface org.molgenis.omx.biobankconnect.ontologyannotator.OntologyAnnotator

UpdateIndexRequest - Class in org.molgenis.omx.biobankconnect.ontologyannotator

UpdateIndexRequest(Integer, String, List<Integer>, List<String>, String) - Constructor for class org.molgenis.omx.biobankconnect.ontologyannotator.UpdateIndexRequest

updateScript(String, OntologyMatcherRequest) - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher

updateScript(String, OntologyMatcherRequest) - Method in interface org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcher

upload(String, Part, Model) - Method in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceController

uploadFeatures(File, String) - Method in class org.molgenis.omx.biobankconnect.ontologyannotator.AsyncOntologyAnnotator

uploadFeatures(File, String) - Method in interface org.molgenis.omx.biobankconnect.ontologyannotator.OntologyAnnotator

URI - Static variable in class org.molgenis.omx.biobankconnect.algorithm.AlgorithmEditorController

URI - Static variable in class org.molgenis.omx.biobankconnect.mappingmanager.MappingManagerController

URI - Static variable in class org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexerController

URI - Static variable in class org.molgenis.omx.biobankconnect.ontologyservice.OntologyServiceController

URI - Static variable in class org.molgenis.omx.biobankconnect.ontologytree.OntologyTreeController

URI - Static variable in class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

V

validateAlgorithmInputs(Integer, String) - Method in class org.molgenis.omx.biobankconnect.algorithm.ApplyAlgorithms

valueOf(String) - Static method in enum org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus.STAGE

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.molgenis.omx.biobankconnect.wizard.CurrentUserStatus.STAGE

Returns an array containing the constants of this enum type, in the order they are declared.

Z

ZipFileUtil - Class in org.molgenis.omx.biobankconnect.utils

ZipFileUtil() - Constructor for class org.molgenis.omx.biobankconnect.utils.ZipFileUtil

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