A B C E G I L M O P R S T

A

appendLine(CharSequence) - Method in class org.geneontology.lego.dot.LegoDotWriter
Write a line to the file.

B

bp - Variable in class org.geneontology.lego.model.LegoTools
 

C

CellularLocationTools - Class in org.geneontology.lego.model
 
CellularLocationTools() - Constructor for class org.geneontology.lego.model.CellularLocationTools
 
close() - Method in class org.geneontology.lego.dot.LegoDotWriter
Overwrite this method to implement a custom close() function for the writer.
createLegoGraph(Collection<OWLNamedIndividual>) - Method in class org.geneontology.lego.model2.LegoUnitTools
 
createLegoNodes(Collection<OWLNamedIndividual>) - Method in class org.geneontology.lego.model.LegoTools
 

E

enabled_by - Variable in class org.geneontology.lego.model.LegoTools
 

G

getActiveEntity() - Method in class org.geneontology.lego.model.LegoNode
 
getActivity() - Method in class org.geneontology.lego.model2.LegoUnit
 
getCellularLocation() - Method in class org.geneontology.lego.model.LegoNode
 
getEnabledBy() - Method in class org.geneontology.lego.model2.LegoUnit
 
getId() - Method in class org.geneontology.lego.model.LegoNode
 
getId() - Method in class org.geneontology.lego.model2.LegoUnit
 
getIndividual() - Method in class org.geneontology.lego.model.LegoNode
 
getLinks() - Method in class org.geneontology.lego.model.LegoNode
 
getLinks() - Method in class org.geneontology.lego.model2.LegoGraph
Extract the whole list of links form the nodes
getLocation() - Method in class org.geneontology.lego.model2.LegoUnit
 
getNamedTarget() - Method in class org.geneontology.lego.model.LegoLink
 
getNodes() - Method in class org.geneontology.lego.model2.LegoGraph
 
getProcess() - Method in class org.geneontology.lego.model2.LegoUnit
 
getProperty() - Method in class org.geneontology.lego.model.LegoLink
 
getSource() - Method in class org.geneontology.lego.model.LegoLink
 
getType() - Method in class org.geneontology.lego.model.LegoNode
 
getUnits() - Method in class org.geneontology.lego.model2.LegoGraph
The units are for display purposes only.
For the full model use nodes and links.
getUnknowns() - Method in class org.geneontology.lego.model.LegoNode
 
graph - Variable in class org.geneontology.lego.model.LegoTools
 

I

ignoreUnknownTypes - Variable in class org.geneontology.lego.model.LegoTools
 
isBp() - Method in class org.geneontology.lego.model.LegoNode
 
isCmf() - Method in class org.geneontology.lego.model.LegoNode
 
isMf() - Method in class org.geneontology.lego.model.LegoNode
 

L

LegoDotWriter - Class in org.geneontology.lego.dot
Rudimentary implementation of a DOT writer for the LEGO annotations in OWL.
LegoDotWriter(OWLGraphWrapper, OWLReasoner) - Constructor for class org.geneontology.lego.dot.LegoDotWriter
Create a new writer for the given ontology and reasoner.
LegoGraph - Class in org.geneontology.lego.model2
 
LegoGraph(List<LegoUnit>, List<LegoNode>) - Constructor for class org.geneontology.lego.model2.LegoGraph
 
LegoLink - Class in org.geneontology.lego.model
 
LegoLink(OWLNamedIndividual, OWLNamedIndividual, OWLObjectPropertyExpression) - Constructor for class org.geneontology.lego.model.LegoLink
 
LegoNode - Class in org.geneontology.lego.model
 
LegoNode(OWLNamedIndividual, OWLClassExpression) - Constructor for class org.geneontology.lego.model.LegoNode
 
LegoRenderer - Interface in org.geneontology.lego.dot
 
LegoShuntGraphTool - Class in org.geneontology.lego.json
Helper to create a shut graph for a given set of lego nodes.

This creates nodes and edges, where the nodes are the individuals with a simple label.
LegoShuntGraphTool() - Constructor for class org.geneontology.lego.json.LegoShuntGraphTool
 
LegoTools - Class in org.geneontology.lego.model
Tool to convert the OWL representation of annotations into the rendering model.
LegoTools(OWLGraphWrapper, OWLReasoner) - Constructor for class org.geneontology.lego.model.LegoTools
 
LegoTools(OWLGraphWrapper, OWLReasoner, boolean) - Constructor for class org.geneontology.lego.model.LegoTools
 
LegoTools(OWLGraphWrapper, OWLReasoner, Set<OWLObjectProperty>, Set<OWLObjectProperty>, Set<OWLObjectProperty>, OWLClass, OWLClass, boolean) - Constructor for class org.geneontology.lego.model.LegoTools
 
LegoTools.UnExpectedStructureException - Exception in org.geneontology.lego.model
 
LegoTools.UnExpectedStructureException(String, Throwable) - Constructor for exception org.geneontology.lego.model.LegoTools.UnExpectedStructureException
 
LegoTools.UnExpectedStructureException(String) - Constructor for exception org.geneontology.lego.model.LegoTools.UnExpectedStructureException
 
LegoUnit - Class in org.geneontology.lego.model2
 
LegoUnit(IRI, OWLClass, OWLClass, OWLClass, List<OWLClass>) - Constructor for class org.geneontology.lego.model2.LegoUnit
 
LegoUnitTools - Class in org.geneontology.lego.model2
 
LegoUnitTools(OWLGraphWrapper, OWLReasoner) - Constructor for class org.geneontology.lego.model2.LegoUnitTools
 

M

mf - Variable in class org.geneontology.lego.model.LegoTools
 

O

occurs_in - Variable in class org.geneontology.lego.model.LegoTools
 
open() - Method in class org.geneontology.lego.dot.LegoDotWriter
Overwrite this method to implement a custom open() routine for the writer.
org.geneontology.lego.dot - package org.geneontology.lego.dot
 
org.geneontology.lego.json - package org.geneontology.lego.json
 
org.geneontology.lego.model - package org.geneontology.lego.model
 
org.geneontology.lego.model2 - package org.geneontology.lego.model2
 

P

part_of - Variable in class org.geneontology.lego.model.LegoTools
 

R

reasoner - Variable in class org.geneontology.lego.model.LegoTools
 
render(Collection<OWLNamedIndividual>, String, boolean) - Method in class org.geneontology.lego.dot.LegoDotWriter
 
render(Collection<OWLNamedIndividual>, String, boolean) - Method in interface org.geneontology.lego.dot.LegoRenderer
Render the given individuals (aka set of annotations).
renderLego(Collection<LegoNode>, String, boolean) - Method in class org.geneontology.lego.dot.LegoDotWriter
Render the given collection of nodes (LegoNode)
renderLego(Collection<LegoNode>, OWLGraphWrapper) - Method in class org.geneontology.lego.json.LegoShuntGraphTool
Render the given collection of nodes (LegoNode)

S

searchCellularLocation(OWLClassExpression, OWLGraphWrapper, Set<OWLObjectProperty>) - Static method in class org.geneontology.lego.model.CellularLocationTools
 
setActiveEntity(OWLClass) - Method in class org.geneontology.lego.model.LegoNode
 
setBp(boolean) - Method in class org.geneontology.lego.model.LegoNode
 
setCellularLocation(Collection<OWLClassExpression>) - Method in class org.geneontology.lego.model.LegoNode
 
setCmf(boolean) - Method in class org.geneontology.lego.model.LegoNode
 
setLinks(Collection<LegoLink>) - Method in class org.geneontology.lego.model.LegoNode
 
setMf(boolean) - Method in class org.geneontology.lego.model.LegoNode
 
setUnknowns(Collection<OWLClassExpression>) - Method in class org.geneontology.lego.model.LegoNode
 
StringTools - Class in org.geneontology.lego.dot
 
StringTools() - Constructor for class org.geneontology.lego.dot.StringTools
 

T

toString() - Method in class org.geneontology.lego.model2.LegoUnit
 

A B C E G I L M O P R S T

Copyright © 2012-2013. All Rights Reserved.