Uses of Class
phenote.datamodel.OntologyException

Packages that use OntologyException

phenote.dataadapter	Generalized methods for creating customized Data Adapters
phenote.datamodel
phenote.util

Uses of OntologyException in phenote.dataadapter

Methods in phenote.dataadapter that throw OntologyException

boolean	OntologyDataAdapter2.checkForUpdate(phenote.config.xml.OntologyFileDocument.OntologyFile ontologyFile)
void	OntologyDataAdapter2.downloadUpdate(java.lang.String ontology)
java.net.URL	OntologyDataAdapter2.getLocalFile(java.lang.String handle)
long	OntologyDataAdapter2.getOboDate(java.net.URL oboUrl)
long	OntologyDataAdapter.getOboDate(java.net.URL oboUrl) Get the date of the file from the header of the obo file - just read header dont read in whole file.
void	OntologyDataAdapter2.reloadOntologies() The ontology has been determined to be out of date (by quartz) and thus directed to reload itself from its file - in other words there is a new obo file to load in place of old one
void	OntologyDataAdapter.reloadOntologies() The ontology has been determined to be out of date (by quartz) and thus directed to reload itself from its file - in other words there is a new obo file to load in place of old one

Uses of OntologyException in phenote.datamodel

Methods in phenote.datamodel that throw OntologyException

CharField	CharFieldManager.getCharField(int i) get char field for int.
CharField	CharFieldManager.getCharField(int i, java.lang.String group)
Ontology	CharFieldManager.getOntologyForTerm(org.obo.datamodel.OBOClass term) Currently iterates through every ontology looking for term, if this proves too inefficient we could do something with ID prefixes

Uses of OntologyException in phenote.util

Methods in phenote.util that throw OntologyException

static void	FileUtil.copyReposToLocal(java.net.URL reposUrl, java.net.URL localUrl) local url may be from distrib/jar dir, but needs to be set to .phenote/obo-files dir as thats where the user cache is
static java.net.URL	FileUtil.findFile(java.lang.String fileName) Look for file in current directory (.) and jar file throws OntologyException if file not found - wraps FileNFEx