Module org.monarchinitiative.hpotextmining.gui

Package org.monarchinitiative.hpotextmining.gui.controller

Class HpoTextMining.HpoTextMiningBuilder

java.lang.Object

org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining.HpoTextMiningBuilder

Enclosing class:

HpoTextMining

public static final class HpoTextMining.HpoTextMiningBuilder
extends Object

Method Summary

Modifier and Type	Method	Description
HpoTextMining	build()
HpoTextMining.HpoTextMiningBuilder	withBiolarkUrl(URL biolarkServerUrl)
HpoTextMining.HpoTextMiningBuilder	withExecutorService(ExecutorService executorService)
HpoTextMining.HpoTextMiningBuilder	withOntology(org.monarchinitiative.phenol.ontology.data.Ontology ontology)
HpoTextMining.HpoTextMiningBuilder	withPhenotypeTerms(Set<Main.PhenotypeTerm> terms)
HpoTextMining.HpoTextMiningBuilder	withSciGraphUrl(URL sciGraphServerUrl)
HpoTextMining.HpoTextMiningBuilder	withTermMiner(TermMiner miner)

Methods inherited from class java.lang.Object

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

Method Details

withOntology

public HpoTextMining.HpoTextMiningBuilder withOntology(org.monarchinitiative.phenol.ontology.data.Ontology ontology)

Parameters:

ontology - Ontology to work with (mandatory)

Returns:

this HpoTextMining.HpoTextMiningBuilder instance

withBiolarkUrl

public HpoTextMining.HpoTextMiningBuilder withBiolarkUrl(URL biolarkServerUrl)

Parameters:

biolarkServerUrl - URL pointing to Biolark server instance where the text mining should be performed. SciGraph URL has precedence

Returns:

this HpoTextMining.HpoTextMiningBuilder instance

withSciGraphUrl

public HpoTextMining.HpoTextMiningBuilder withSciGraphUrl(URL sciGraphServerUrl)

Parameters:

sciGraphServerUrl - URL pointing to SciGraph server instance where the text mining should be performed. SciGraph URL has precedence over Biolark URL

Returns:

this HpoTextMining.HpoTextMiningBuilder instance

withTermMiner

public HpoTextMining.HpoTextMiningBuilder withTermMiner(TermMiner miner)

Parameters:

miner - TermMiner to use for the text mining analysis. The miner has precedence over any URL (SciGraph, Biolark, etc..)

Returns:

this HpoTextMining.HpoTextMiningBuilder instance

withExecutorService

public HpoTextMining.HpoTextMiningBuilder withExecutorService(ExecutorService executorService)

Parameters:

executorService - ExecutorService to be used for asynchronous tasks (optional)

Returns:

this HpoTextMining.HpoTextMiningBuilder instance

withPhenotypeTerms

public HpoTextMining.HpoTextMiningBuilder withPhenotypeTerms(Set<Main.PhenotypeTerm> terms)

Parameters:

terms - Set of terms to display in the widget from the beginning

Returns:

this HpoTextMining.HpoTextMiningBuilder instance

build

public HpoTextMining build()
                    throws IOException

Returns:

a new HpoTextMining instance

Throws:

IOException - in case if the building fails