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

A

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

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

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

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

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

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() - 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.BoostTermContainer - Class in org.molgenis.omx.biobankconnect.ontologymatcher

AsyncOntologyMatcher.BoostTermContainer(String, LinkedHashSet<String>, boolean) - Constructor for class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher.BoostTermContainer

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, ProgressingBarPage) - Constructor for class org.molgenis.omx.biobankconnect.wizard.BiobankConnectController

BiobankConnectHomeController - Class in org.molgenis.omx.biobankconnect.controllers

BiobankConnectHomeController() - Constructor for class org.molgenis.omx.biobankconnect.controllers.BiobankConnectHomeController

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

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.utils.OntologyRepository

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

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

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

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.utils.OntologyRepository

count() - Method in class org.molgenis.omx.biobankconnect.utils.OntologyTermRepository

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

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

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

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

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

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

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

deleteDocuments(UpdateIndexRequest) - Method in class org.molgenis.omx.biobankconnect.mappingmanager.MappingManagerController

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(String, HttpServletResponse) - Method in class org.molgenis.omx.biobankconnect.mappingmanager.MappingManagerController

E

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

EvaluationController - Class in org.molgenis.omx.biobankconnect.evaluation

EvaluationController(SearchService, DataService) - Constructor for class org.molgenis.omx.biobankconnect.evaluation.EvaluationController

F

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

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

G

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

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

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

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

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

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

getEntityClass() - Method in class org.molgenis.omx.biobankconnect.utils.OntologyRepository

getEntityClass() - Method in class org.molgenis.omx.biobankconnect.utils.OntologyTermRepository

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

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

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

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

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

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

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

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

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

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

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.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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.OntologyMatcherResponse

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

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.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

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

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

I

ID - Static variable in class org.molgenis.omx.biobankconnect.evaluation.EvaluationController

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

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

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

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

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

index(String, File) - Method in class org.molgenis.omx.biobankconnect.ontologyindexer.AsyncOntologyIndexer

index(String, File) - Method in interface org.molgenis.omx.biobankconnect.ontologyindexer.OntologyIndexer

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

init(Model) - Method in class org.molgenis.omx.biobankconnect.controllers.BiobankConnectHomeController

init(String, Model) - Method in class org.molgenis.omx.biobankconnect.evaluation.EvaluationController

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

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

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

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

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

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.AsyncOntologyMatcher

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

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

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.utils.OntologyRepository

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

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

L

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, SearchService, 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

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

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

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

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

O

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

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

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

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>) - Constructor for class org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcherRequest

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

OntologyMatcherResponse(String, Boolean, Integer, Integer) - Constructor for class org.molgenis.omx.biobankconnect.ontologymatcher.OntologyMatcherResponse

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

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

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

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

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

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

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

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

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

P

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

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

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

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

S

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

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

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

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

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

setBoost(boolean) - Method in class org.molgenis.omx.biobankconnect.ontologymatcher.AsyncOntologyMatcher.BoostTermContainer

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.ontologyindexer.AsyncOntologyIndexer

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

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

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

T

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

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

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

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

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

U

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

updateDocument(UpdateIndexRequest) - Method in class org.molgenis.omx.biobankconnect.mappingmanager.MappingManagerController

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

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.controllers.BiobankConnectHomeController

URI - Static variable in class org.molgenis.omx.biobankconnect.evaluation.EvaluationController

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.wizard.BiobankConnectController

V

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.

verify(String, Part, HttpServletResponse, Model) - Method in class org.molgenis.omx.biobankconnect.evaluation.EvaluationController

Z

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

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

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