B C E F G H I J L M O P R T W

B

build() - Method in class org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining.HpoTextMiningBuilder

builder() - Static method in class org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining

C

Configure - Class in org.monarchinitiative.hpotextmining.gui.controller

Controller for the part of the dialog that controls entering of text that will be mined for HPO terms along with PMID of a publication.

confirmAndClose() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Main

E

equals(Object) - Method in class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

F

focusToTerm(String) - Method in class org.monarchinitiative.hpotextmining.gui.controller.Present.JavaBridge

G

getApprovedTerms() - Method in class org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining

getBegin() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

getEnd() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

getMainParent() - Method in class org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining

getTerm() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

H

hashCode() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

HpoTextMining - Class in org.monarchinitiative.hpotextmining.gui.controller

Driver class/API for JavaFX presentation of HPO text mining.

HpoTextMining.HpoTextMiningBuilder - Class in org.monarchinitiative.hpotextmining.gui.controller

I

initialize() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Configure

Initialize GUI elements after processing by FXMLLoader.

initialize() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Main

Initialize JavaFX components of Main controller.

initialize() - Method in class org.monarchinitiative.hpotextmining.gui.controller.OntologyTree

Populate the OntologyTree.ontologyTreeView with the root Terms of provided Ontology.

initialize() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Present

isPresent() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

J

JavaBridge() - Constructor for class org.monarchinitiative.hpotextmining.gui.controller.Present.JavaBridge

L

leftStackPane - Variable in class org.monarchinitiative.hpotextmining.gui.controller.Main

Ontology is presented here by OntologyTree controller.

log(String) - Method in class org.monarchinitiative.hpotextmining.gui.controller.Present.JavaBridge

M

Main - Class in org.monarchinitiative.hpotextmining.gui.controller

This class acts as the controller of the main dialog window of the HpoTextMining analysis dialog.

Main() - Constructor for class org.monarchinitiative.hpotextmining.gui.controller.Main

Create the controller.

Main.PhenotypeTerm - Class in org.monarchinitiative.hpotextmining.gui.controller

O

OntologyTree - Class in org.monarchinitiative.hpotextmining.gui.controller

This class acts as the controller of the Pane on the left side of the main HPO dialog.

OntologyTree(Ontology, Consumer<Main.PhenotypeTerm>) - Constructor for class org.monarchinitiative.hpotextmining.gui.controller.OntologyTree

org.monarchinitiative.hpotextmining.gui.controller - package org.monarchinitiative.hpotextmining.gui.controller

P

PhenotypeTerm(Term, MinedTerm) - Constructor for class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

PhenotypeTerm(Term, boolean) - Constructor for class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

PhenotypeTerm(Term, int, int, boolean) - Constructor for class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

PhenotypeTerm(Main.PhenotypeTerm, boolean) - Constructor for class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

Present - Class in org.monarchinitiative.hpotextmining.gui.controller

This class is responsible for displaying the terms of performed text-mining analysis.

Present.JavaBridge - Class in org.monarchinitiative.hpotextmining.gui.controller

This class is the bridge between JavaScript run in the Present.webView and Java code.

R

removeTermButtonAction() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Main

T

toString() - Method in class org.monarchinitiative.hpotextmining.gui.controller.Main.PhenotypeTerm

W

withBiolarkUrl(URL) - Method in class org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining.HpoTextMiningBuilder

withExecutorService(ExecutorService) - Method in class org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining.HpoTextMiningBuilder

withOntology(Ontology) - Method in class org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining.HpoTextMiningBuilder

withPhenotypeTerms(Set<Main.PhenotypeTerm>) - Method in class org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining.HpoTextMiningBuilder

withSciGraphUrl(URL) - Method in class org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining.HpoTextMiningBuilder

withTermMiner(TermMiner) - Method in class org.monarchinitiative.hpotextmining.gui.controller.HpoTextMining.HpoTextMiningBuilder

B C E F G H I J L M O P R T W