org.geneontology.lego.model
Class LegoTools

java.lang.Object
  extended by org.geneontology.lego.model.LegoTools
Direct Known Subclasses:
LegoUnitTools

public class LegoTools
extends Object

Tool to convert the OWL representation of annotations into the rendering model.

See Also:
LegoNode, LegoLink

Nested Class Summary
static class LegoTools.UnExpectedStructureException
           
 
Field Summary
protected  org.semanticweb.owlapi.model.OWLClass bp
           
protected  Set<org.semanticweb.owlapi.model.OWLObjectProperty> enabled_by
           
protected  owltools.graph.OWLGraphWrapper graph
           
protected  boolean ignoreUnknownTypes
           
protected  org.semanticweb.owlapi.model.OWLClass mf
           
protected  Set<org.semanticweb.owlapi.model.OWLObjectProperty> occurs_in
           
protected  Set<org.semanticweb.owlapi.model.OWLObjectProperty> part_of
           
protected  org.semanticweb.owlapi.reasoner.OWLReasoner reasoner
           
 
Constructor Summary
  LegoTools(owltools.graph.OWLGraphWrapper graph, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
           
  LegoTools(owltools.graph.OWLGraphWrapper graph, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, boolean ignoreUnknownTypes)
           
protected LegoTools(owltools.graph.OWLGraphWrapper graph, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, Set<org.semanticweb.owlapi.model.OWLObjectProperty> enabled_by, Set<org.semanticweb.owlapi.model.OWLObjectProperty> occurs_in, Set<org.semanticweb.owlapi.model.OWLObjectProperty> part_of, org.semanticweb.owlapi.model.OWLClass mf, org.semanticweb.owlapi.model.OWLClass bp, boolean ignoreUnknownTypes)
           
 
Method Summary
 List<LegoNode> createLegoNodes(Collection<org.semanticweb.owlapi.model.OWLNamedIndividual> individuals)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

graph

protected final owltools.graph.OWLGraphWrapper graph

reasoner

protected final org.semanticweb.owlapi.reasoner.OWLReasoner reasoner

enabled_by

protected final Set<org.semanticweb.owlapi.model.OWLObjectProperty> enabled_by

occurs_in

protected final Set<org.semanticweb.owlapi.model.OWLObjectProperty> occurs_in

part_of

protected final Set<org.semanticweb.owlapi.model.OWLObjectProperty> part_of

mf

protected final org.semanticweb.owlapi.model.OWLClass mf

bp

protected final org.semanticweb.owlapi.model.OWLClass bp

ignoreUnknownTypes

protected final boolean ignoreUnknownTypes
Constructor Detail

LegoTools

public LegoTools(owltools.graph.OWLGraphWrapper graph,
                 org.semanticweb.owlapi.reasoner.OWLReasoner reasoner)
Parameters:
graph -
reasoner -

LegoTools

public LegoTools(owltools.graph.OWLGraphWrapper graph,
                 org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                 boolean ignoreUnknownTypes)
Parameters:
graph -
reasoner -
ignoreUnknownTypes -

LegoTools

protected LegoTools(owltools.graph.OWLGraphWrapper graph,
                    org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
                    Set<org.semanticweb.owlapi.model.OWLObjectProperty> enabled_by,
                    Set<org.semanticweb.owlapi.model.OWLObjectProperty> occurs_in,
                    Set<org.semanticweb.owlapi.model.OWLObjectProperty> part_of,
                    org.semanticweb.owlapi.model.OWLClass mf,
                    org.semanticweb.owlapi.model.OWLClass bp,
                    boolean ignoreUnknownTypes)
Parameters:
graph -
reasoner -
enabled_by -
occurs_in -
part_of -
mf -
bp -
ignoreUnknownTypes -
Method Detail

createLegoNodes

public List<LegoNode> createLegoNodes(Collection<org.semanticweb.owlapi.model.OWLNamedIndividual> individuals)
                               throws LegoTools.UnExpectedStructureException
Throws:
LegoTools.UnExpectedStructureException


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