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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
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