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A B C E G I L M O P R S T U 

A

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

B

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

C

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

E

enabled_by - Variable in class org.geneontology.lego.model.LegoTools
Deprecated.
 
extractMetadata(LegoMetadata, Iterable<? extends OWLAxiom>) - Static method in class org.geneontology.lego.model.LegoMetadata
Deprecated.
 
extractMetadata(LegoMetadata, OWLAxiom) - Static method in class org.geneontology.lego.model.LegoMetadata
Deprecated.
 

G

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

I

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

L

LegoDotWriter - Class in org.geneontology.lego.dot
Deprecated.
LegoDotWriter(OWLGraphWrapper, OWLReasoner) - Constructor for class org.geneontology.lego.dot.LegoDotWriter
Deprecated.
Create a new writer for the given ontology and reasoner.
LegoGraph - Class in org.geneontology.lego.model2
Deprecated.
LegoGraph(List<LegoUnit>, List<LegoNode>, String) - Constructor for class org.geneontology.lego.model2.LegoGraph
Deprecated.
 
LegoLink - Class in org.geneontology.lego.model
Deprecated.
LegoLink(OWLNamedIndividual, OWLNamedIndividual, OWLObjectPropertyExpression) - Constructor for class org.geneontology.lego.model.LegoLink
Deprecated.
 
LegoMetadata - Class in org.geneontology.lego.model
Deprecated.
LegoMetadata() - Constructor for class org.geneontology.lego.model.LegoMetadata
Deprecated.
 
LegoNode - Class in org.geneontology.lego.model
Deprecated.
LegoNode(OWLNamedIndividual, OWLClassExpression) - Constructor for class org.geneontology.lego.model.LegoNode
Deprecated.
 
LegoRenderer - Interface in org.geneontology.lego.dot
Deprecated.
LegoShuntGraphTool - Class in org.geneontology.lego.json
Deprecated.
LegoShuntGraphTool() - Constructor for class org.geneontology.lego.json.LegoShuntGraphTool
Deprecated.
 
LegoTools - Class in org.geneontology.lego.model
Deprecated.
LegoTools(OWLGraphWrapper, OWLReasoner) - Constructor for class org.geneontology.lego.model.LegoTools
Deprecated.
 
LegoTools(OWLGraphWrapper, OWLReasoner, boolean) - Constructor for class org.geneontology.lego.model.LegoTools
Deprecated.
 
LegoTools(OWLGraphWrapper, OWLReasoner, Set<OWLObjectProperty>, Set<OWLObjectProperty>, Set<OWLObjectProperty>, OWLClass, OWLClass, boolean) - Constructor for class org.geneontology.lego.model.LegoTools
Deprecated.
 
LegoTools.UnExpectedStructureException - Exception in org.geneontology.lego.model
Deprecated.
 
LegoUnit - Class in org.geneontology.lego.model2
Deprecated.
LegoUnit(IRI, OWLClass, OWLClass, OWLClass, List<OWLClass>) - Constructor for class org.geneontology.lego.model2.LegoUnit
Deprecated.
 
LegoUnitTools - Class in org.geneontology.lego.model2
Deprecated.
LegoUnitTools(OWLGraphWrapper, OWLReasoner) - Constructor for class org.geneontology.lego.model2.LegoUnitTools
Deprecated.
 

M

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

O

occurs_in - Variable in class org.geneontology.lego.model.LegoTools
Deprecated.
 
open() - Method in class org.geneontology.lego.dot.LegoDotWriter
Deprecated.
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
Deprecated.
 

R

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

S

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

T

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

U

UnExpectedStructureException(String, Throwable) - Constructor for exception org.geneontology.lego.model.LegoTools.UnExpectedStructureException
Deprecated.
 
UnExpectedStructureException(String) - Constructor for exception org.geneontology.lego.model.LegoTools.UnExpectedStructureException
Deprecated.
 
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