Deprecated API

Contents

• Packages
• Classes
• Methods

Deprecated Packages

Package	Description
com.github.fommil.netlib	use invalid reference dev.ludovic.netlib instead

Deprecated Classes

Class	Description
com.github.fommil.netlib.ARPACK	use ARPACK instead
com.github.fommil.netlib.BLAS	use BLAS instead
com.github.fommil.netlib.LAPACK	use LAPACK instead
ubic.basecode.ontology.providers.DiseaseOntologyService	use MONDO instead
ubic.basecode.ontology.providers.FMAOntologyService	this ontology is inactive, use UBERON instead
ubic.basecode.ontology.providers.HumanDevelopmentOntologyService	this ontology was last updated in unmaintained since 2013
ubic.basecode.ontology.providers.MedicOntologyService
ubic.basecode.ontology.providers.NIFSTDOntologyService

Deprecated Methods

Method	Description
ubic.basecode.ontology.model.OntologyTerm.getTerm()	use OntologyResource.getLabel() instead.
ubic.basecode.ontology.model.OntologyTerm.isTermObsolete()	use OntologyResource.isObsolete() instead
ubic.basecode.ontology.providers.AbstractDelegatingOntologyService.loadTermsInNameSpace(InputStream, boolean)
ubic.basecode.ontology.providers.OntologyService.loadTermsInNameSpace(InputStream, boolean)	use OntologyService.initialize(InputStream, boolean) instead and possibly OntologyService.cancelInitializationThread() prior to get any running initialization thread out of the way
ubic.basecode.util.StringUtil.makeValidForR(String)	use StringUtil.makeNames(String[], boolean) instead
ubic.basecode.util.StringUtil.makeValidForR(String[])	use StringUtil.makeNames(String[], boolean) instead