Uses of Class
org.molgenis.vibe.core.formats.Phenotype

Packages that use Phenotype

Package	Description
org.molgenis.vibe.core
org.molgenis.vibe.core.formats
org.molgenis.vibe.core.ontology_processing
org.molgenis.vibe.core.tdb_processing
org.molgenis.vibe.core.tdb_processing.query_string_creation

Uses of Phenotype in org.molgenis.vibe.core

Constructor parameters in org.molgenis.vibe.core with type arguments of type Phenotype

Constructor	Description
GeneDiseaseCollectionRetrievalRunner(Path vibeTdb, Set<Phenotype> phenotypes)
PhenotypesRetrievalRunner(Path hpoOntologyFile, PhenotypesRetrieverFactory phenotypesRetrieverFactory, Collection<Phenotype> phenotypes, Integer maxDistance)

Uses of Phenotype in org.molgenis.vibe.core.formats

Methods in org.molgenis.vibe.core.formats that return Phenotype

Modifier and Type	Method	Description
Phenotype	PhenotypeNetwork.getSource()

Methods in org.molgenis.vibe.core.formats that return types with arguments of type Phenotype

Modifier and Type	Method	Description
Set<Phenotype>	PhenotypeNetwork.getByDistance(int distance)	Retrieves all Phenotypes that have the specified distance
Set<Phenotype>	PhenotypeNetwork.getPhenotypes()
Set<Phenotype>	PhenotypeNetworkCollection.getPhenotypes()

Methods in org.molgenis.vibe.core.formats with parameters of type Phenotype

Modifier and Type	Method	Description
boolean	PhenotypeNetwork.add(Phenotype phenotype, int distance)	Adds a Phenotype to the PhenotypeNetwork.
boolean	PhenotypeNetwork.contains(Phenotype phenotype)
int	PhenotypeNetwork.getDistance(Phenotype phenotype)	Retrieve the stored distance belonging to a Phenotype
PhenotypeNetwork	PhenotypeNetworkCollection.getPhenotypeNetworkBySource(Phenotype source)	Retrieve a PhenotypeNetwork based on its PhenotypeNetwork.getSource().
PhenotypeNetwork	PhenotypeNetworkCollection.remove(Phenotype phenotypeSource)	Removes a PhenotypeNetwork from the PhenotypeNetworkCollection.

Method parameters in org.molgenis.vibe.core.formats with type arguments of type Phenotype

Modifier and Type	Method	Description
void	PhenotypeNetwork.add(Collection<Phenotype> phenotypes, int distance)

Constructors in org.molgenis.vibe.core.formats with parameters of type Phenotype

Constructor	Description
PhenotypeNetwork(Phenotype phenotype)

Uses of Phenotype in org.molgenis.vibe.core.ontology_processing

Methods in org.molgenis.vibe.core.ontology_processing that return types with arguments of type Phenotype

Modifier and Type	Method	Description
Collection<Phenotype>	PhenotypesRetriever.getInputPhenotypes()

Methods in org.molgenis.vibe.core.ontology_processing with parameters of type Phenotype

Modifier and Type	Method	Description
protected org.apache.jena.ontology.OntClass	PhenotypesRetriever.retrievePhenotypeFromModel(Phenotype phenotype)

Method parameters in org.molgenis.vibe.core.ontology_processing with type arguments of type Phenotype

Modifier and Type	Method	Description
abstract PhenotypesRetriever	PhenotypesRetrieverFactory.create(org.apache.jena.ontology.OntModel model, Collection<Phenotype> inputPhenotypes, int distance)

Constructor parameters in org.molgenis.vibe.core.ontology_processing with type arguments of type Phenotype

Constructor	Description
ChildrenRetriever(org.apache.jena.ontology.OntModel model, Collection<Phenotype> inputPhenotypes, int maxDistance)
MaxDistanceRetriever(org.apache.jena.ontology.OntModel model, Collection<Phenotype> inputPhenotypes, int maxDistance)
PhenotypesRetriever(org.apache.jena.ontology.OntModel model, Collection<Phenotype> inputPhenotypes, int maxDistance)

Uses of Phenotype in org.molgenis.vibe.core.tdb_processing

Constructor parameters in org.molgenis.vibe.core.tdb_processing with type arguments of type Phenotype

Constructor	Description
GenesForPhenotypeRetriever(ModelReader modelReader, Set<Phenotype> phenotypes)

Uses of Phenotype in org.molgenis.vibe.core.tdb_processing.query_string_creation

Method parameters in org.molgenis.vibe.core.tdb_processing.query_string_creation with type arguments of type Phenotype

Modifier and Type	Method	Description
static QueryString	QueryStringGenerator.getGenesForPhenotypes(Set<Phenotype> phenotypes)