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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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