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Uses of Class
macaw.businessLayer.OntologyTerm

Packages that use OntologyTerm
macaw.businessLayer Contains classes that represent business concepts in the system. 
macaw.persistenceLayer Contains the main APIs used by other software clients. 
macaw.persistenceLayer.demo This package contains all the code required to run versions of Macaw's curation and retrieval services which store data in-memory. 
macaw.persistenceLayer.production This package contains all the code required to run versions of Macaw's curation and retrieval services which store data in a MySQL database. 
macaw.presentationLayer This is the main package that produces the GUI application forms for Macaw. 
 

Uses of OntologyTerm in macaw.businessLayer
 

Methods in macaw.businessLayer that return types with arguments of type OntologyTerm
 java.util.ArrayList<OntologyTerm> MacawCurationAPI.filterOntologyTerms(User user, java.lang.String term, java.lang.String description)
           
 java.util.ArrayList<OntologyTerm> MacawCurationAPI.getAllOntologyTerms(User user)
           
 java.util.ArrayList<OntologyTerm> Variable.getOntologyTerms()
           
 java.util.ArrayList<OntologyTerm> MacawRetrievalAPI.getOntologyTerms(User user, java.lang.String variableName)
          return the ontology terms for a given variable
 java.util.ArrayList<OntologyTerm> MacawCurationAPI.getOntologyTerms(User user, Variable variable)
           
 

Methods in macaw.businessLayer with parameters of type OntologyTerm
 void Variable.addOntologyTerm(OntologyTerm ontologyTerm)
           
 void MacawCurationAPI.addOntologyTerm(User user, OntologyTerm ontologyTerm)
           
 boolean Variable.containsOntologyTerm(OntologyTerm targetOntologyTerm)
           
static java.util.ArrayList<MacawChangeEvent> OntologyTerm.detectFieldChanges(User user, OntologyTerm originalOntologyTerm, OntologyTerm revisedOntologyTerm)
           
 int MacawCurationAPI.getOntologyTermIdentifier(User user, OntologyTerm ontologyTerm)
           
 boolean OntologyTerm.hasSameDisplayName(OntologyTerm ontologyTerm)
           
 void Variable.removeOntologyTerm(OntologyTerm copyOfOntologyTermToDelete)
           
 void Variable.updateOntologyTerm(OntologyTerm revisedOntologyTerm)
           
 void MacawCurationAPI.updateOntologyTerm(User user, OntologyTerm ontologyTerm)
           
static void OntologyTerm.validateFields(OntologyTerm ontologyTerm)
           
 

Method parameters in macaw.businessLayer with type arguments of type OntologyTerm
 void Variable.addOntologyTerms(java.util.ArrayList<OntologyTerm> ontologyTermsToAdd)
           
 void MacawCurationAPI.associateOntologyTermsWithVariable(User user, Variable variable, java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 void MacawCurationAPI.deleteOntologyTerms(User user, java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 void MacawCurationAPI.disassociateOntologyTermsFromVariable(User user, Variable variable, java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 void Variable.removeOntologyTerms(java.util.ArrayList<OntologyTerm> ontologyTermsToDelete)
           
 void Variable.setOntologyTerms(java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 

Uses of OntologyTerm in macaw.persistenceLayer
 

Methods in macaw.persistenceLayer with parameters of type OntologyTerm
static java.util.ArrayList<MacawChangeEvent> ChangeEventGenerator.addOntologyTermChange(User user, OntologyTerm ontologyTerm)
          produce change events for operations which involve adding ontology terms to the database
 

Method parameters in macaw.persistenceLayer with type arguments of type OntologyTerm
static java.util.ArrayList<MacawChangeEvent> ChangeEventGenerator.deleteOntologyTermsChange(User user, java.util.ArrayList<OntologyTerm> ontologyTerms)
          produce change events for operations which involve deleting ontology terms from the database
 

Uses of OntologyTerm in macaw.persistenceLayer.demo
 

Methods in macaw.persistenceLayer.demo that return OntologyTerm
 OntologyTerm InMemoryOntologyTermManager.getOriginalOntologyTerm(OntologyTerm ontologyTerm)
           
 

Methods in macaw.persistenceLayer.demo that return types with arguments of type OntologyTerm
 java.util.ArrayList<OntologyTerm> InMemoryOntologyTermFilter.filterOntologyTerms(User user, java.lang.String ontologyTermFilter, java.lang.String ontologyDescriptionFilter)
          finds ontology terms that match based on term and based on description.
 java.util.ArrayList<OntologyTerm> DemonstrationCurationService.filterOntologyTerms(User user, java.lang.String termFilter, java.lang.String descriptionFilter)
           
 java.util.ArrayList<OntologyTerm> InMemoryOntologyTermManager.getAllOntologyTerms(User user)
           
 java.util.ArrayList<OntologyTerm> DemonstrationCurationService.getAllOntologyTerms(User user)
           
 java.util.ArrayList<OntologyTerm> InMemoryVariableManager.getAssociatedOntologyTerms(User user, Variable variable)
          public Variable getVariable(User user, String variableName) throws MacawException { if (variableName == null) { return null; } for (Variable variable : variables) { if (variable.getName().equals(variableName) == true) { return variable; } } return null; }
 java.util.ArrayList<OntologyTerm> DemonstrationRetrievalService.getOntologyTerms(User user, java.lang.String variableName)
           
 java.util.ArrayList<OntologyTerm> DemonstrationCurationService.getOntologyTerms(User user, Variable variable)
           
 

Methods in macaw.persistenceLayer.demo with parameters of type OntologyTerm
 void InMemoryOntologyTermManager.addOntologyTerm(User user, OntologyTerm ontologyTerm)
           
 void DemonstrationCurationService.addOntologyTerm(User user, OntologyTerm ontologyTerm)
           
 void InMemoryOntologyTermManager.checkOntologyTermExists(OntologyTerm ontologyTerm)
           
 int InMemoryOntologyTermManager.getOntologyTermIdentifier(OntologyTerm ontologyTerm)
           
 int DemonstrationCurationService.getOntologyTermIdentifier(User user, OntologyTerm ontologyTerm)
           
 OntologyTerm InMemoryOntologyTermManager.getOriginalOntologyTerm(OntologyTerm ontologyTerm)
           
 void InMemoryOntologyTermManager.updateOntologyTerm(User user, OntologyTerm revisedOntologyTerm)
           
 void DemonstrationCurationService.updateOntologyTerm(User user, OntologyTerm ontologyTerm)
           
 void InMemoryVariableManager.updateOntologyTermReferences(OntologyTerm targetOntologyTerm)
           
 

Method parameters in macaw.persistenceLayer.demo with type arguments of type OntologyTerm
 void InMemoryVariableManager.associateOntologyTerms(User user, Variable variable, java.util.ArrayList<OntologyTerm> ontologyTermsToAssociate)
           
 void DemonstrationCurationService.associateOntologyTermsWithVariable(User user, Variable variable, java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 void InMemoryVariableManager.deleteOntologyTermReferences(java.util.ArrayList<OntologyTerm> targetOntologyTerms)
           
 void InMemoryOntologyTermManager.deleteOntologyTerms(User user, java.util.ArrayList<OntologyTerm> ontologyTermsToDelete)
           
 void DemonstrationCurationService.deleteOntologyTerms(User user, java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 void InMemoryVariableManager.disassociateOntologyTerms(User user, Variable variable, java.util.ArrayList<OntologyTerm> ontologyTermsToDisassociate)
           
 void DemonstrationCurationService.disassociateOntologyTermsFromVariable(User user, Variable variable, java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 void InMemoryOntologyTermFilter.setOntologyTerms(java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 

Uses of OntologyTerm in macaw.persistenceLayer.production
 

Methods in macaw.persistenceLayer.production that return OntologyTerm
 OntologyTerm SQLOntologyTermManager.getOriginalOntologyTerm(java.sql.Connection connection, OntologyTerm targetOntologyTerm)
           
 

Methods in macaw.persistenceLayer.production that return types with arguments of type OntologyTerm
 java.util.ArrayList<OntologyTerm> SQLFilterQueries.filterOntologyTerms(java.sql.Connection connection, java.lang.String term, java.lang.String description)
           
 java.util.ArrayList<OntologyTerm> ProductionCurationService.filterOntologyTerms(User user, java.lang.String term, java.lang.String description)
           
 java.util.ArrayList<OntologyTerm> SQLOntologyTermManager.getAllOntologyTerms(java.sql.Connection connection, User user)
           
 java.util.ArrayList<OntologyTerm> ProductionCurationService.getAllOntologyTerms(User user)
           
 java.util.ArrayList<OntologyTerm> SQLVariableManager.getAssociatedOntologyTerms(java.sql.Connection connection, User user, java.lang.String variableName)
           
 java.util.ArrayList<OntologyTerm> SQLVariableManager.getAssociatedOntologyTerms(java.sql.Connection connection, User user, Variable variable)
           
 java.util.ArrayList<OntologyTerm> ProductionRetrievalService.getOntologyTerms(User user, java.lang.String variableName)
           
 java.util.ArrayList<OntologyTerm> ProductionRetrievalService.getOntologyTerms(User user, Variable variable)
           
 java.util.ArrayList<OntologyTerm> ProductionCurationService.getOntologyTerms(User user, Variable variable)
           
 

Methods in macaw.persistenceLayer.production with parameters of type OntologyTerm
 void SQLOntologyTermManager.addOntologyTerm(java.sql.Connection connection, User user, OntologyTerm ontologyTerm)
           
 void ProductionCurationService.addOntologyTerm(User user, OntologyTerm ontologyTerm)
           
 void SQLOntologyTermManager.checkOntologyTermExists(java.sql.Connection connection, OntologyTerm targetOntologyTerm)
           
 int SQLOntologyTermManager.getOntologyTermIdentifier(java.sql.Connection connection, OntologyTerm targetOntologyTerm)
           
 int ProductionCurationService.getOntologyTermIdentifier(User user, OntologyTerm ontologyTerm)
           
 OntologyTerm SQLOntologyTermManager.getOriginalOntologyTerm(java.sql.Connection connection, OntologyTerm targetOntologyTerm)
           
 void SQLOntologyTermManager.updateOntologyTerm(java.sql.Connection connection, User user, OntologyTerm revisedOntologyTerm)
           
 void ProductionCurationService.updateOntologyTerm(User user, OntologyTerm ontologyTerm)
           
 

Method parameters in macaw.persistenceLayer.production with type arguments of type OntologyTerm
 void SQLVariableManager.associateOntologyTerms(java.sql.Connection connection, User user, Variable variable, java.util.ArrayList<OntologyTerm> ontologyTermsToAssociate)
           
 void ProductionCurationService.associateOntologyTermsWithVariable(User user, Variable variable, java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 void SQLOntologyTermManager.deleteOntologyTerms(java.sql.Connection connection, User user, java.util.ArrayList<OntologyTerm> ontologyTermsToDelete)
           
 void ProductionCurationService.deleteOntologyTerms(User user, java.util.ArrayList<OntologyTerm> ontologyTermsToDelete)
           
 void SQLVariableManager.disassociateOntologyTerms(java.sql.Connection connection, User user, Variable variable, java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 void ProductionCurationService.disassociateOntologyTermsFromVariable(User user, Variable variable, java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 

Uses of OntologyTerm in macaw.presentationLayer
 

Methods in macaw.presentationLayer that return OntologyTerm
 OntologyTerm OntologyTermSearchTableModel.getRow(int row)
           
 

Methods in macaw.presentationLayer that return types with arguments of type OntologyTerm
 java.util.ArrayList<OntologyTerm> OntologyTermsPanel.getOntologyTerms()
           
 

Methods in macaw.presentationLayer with parameters of type OntologyTerm
 void OntologyTermEditor.setOntologyTerm(OntologyTerm ontologyTerm)
           
 

Method parameters in macaw.presentationLayer with type arguments of type OntologyTerm
 void OntologyTermSearchTableModel.setData(java.util.ArrayList<OntologyTerm> ontologyTerms)
           
 

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