Package org.molgenis.vibe.core.ontology_processing

Class PhenotypesRetriever

java.lang.Object

org.molgenis.vibe.core.ontology_processing.PhenotypesRetriever

Direct Known Subclasses:

ChildrenRetriever, MaxDistanceRetriever

public abstract class PhenotypesRetriever
extends Object

For one or more Phenotypes within an OntModel, retrieves other Phenotypes that are linked to it.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
protected void	addPhenotypeToNetwork(org.apache.jena.ontology.OntClass phenotypeOC, PhenotypeNetwork network, int distance)	Adds a OntClass representing a Phenotype to a PhenotypeNetwork.
Collection<Phenotype>	getInputPhenotypes()
int	getMaxDistance()
PhenotypeNetworkCollection	getPhenotypeNetworkCollection()
protected org.apache.jena.ontology.OntClass	retrievePhenotypeFromModel(Phenotype phenotype)
abstract void	run()
protected boolean	skippableUri(org.apache.jena.ontology.OntClass phenotypeOC)	Checks whether an URI is skippable.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PhenotypesRetriever

public PhenotypesRetriever(org.apache.jena.ontology.OntModel model,
                           Collection<Phenotype> inputPhenotypes,
                           int maxDistance)

Method Detail

getInputPhenotypes

public Collection<Phenotype> getInputPhenotypes()

getPhenotypeNetworkCollection

public PhenotypeNetworkCollection getPhenotypeNetworkCollection()

getMaxDistance

public int getMaxDistance()

retrievePhenotypeFromModel

protected org.apache.jena.ontology.OntClass retrievePhenotypeFromModel(Phenotype phenotype)

run

public abstract void run()

skippableUri

protected boolean skippableUri(org.apache.jena.ontology.OntClass phenotypeOC)

Checks whether an URI is skippable. This is based on the fact that while the URI is an expected result, it is not used within the application. Otherwise these URIs could cause an error because they would be treated as an unexpected result.

Parameters:

phenotypeOC - the OntClass representing a Phenotype that needs to be checked

Returns:

true if OntClass can be skipped (expected non-valid Phenotype URI), false if not (can either be a valid or an unexpected non-valid Phenotype URI)

addPhenotypeToNetwork

protected void addPhenotypeToNetwork(org.apache.jena.ontology.OntClass phenotypeOC,
                                     PhenotypeNetwork network,
                                     int distance)

Adds a OntClass representing a Phenotype to a PhenotypeNetwork.

Parameters:

phenotypeOC - what needs to be added to the network

network - where the phenotypeOC needs to be added to

distance - the number to be used as distance when adding the phenotypeOC to the network