public class LegoToGeneAnnotationTranslator extends Object
Modifier and Type | Class and Description |
---|---|
protected static class |
AbstractLegoTranslator.BioentityStrings |
protected static class |
AbstractLegoTranslator.Entry<T> |
protected static class |
AbstractLegoTranslator.Metadata |
Modifier and Type | Field and Description |
---|---|
protected org.semanticweb.owlapi.model.OWLClass |
bp |
protected Set<org.semanticweb.owlapi.model.OWLClass> |
bpSet |
protected org.semanticweb.owlapi.model.OWLClass |
cc |
protected Set<org.semanticweb.owlapi.model.OWLClass> |
ccSet |
protected org.semanticweb.owlapi.model.OWLAnnotationProperty |
contributor |
protected org.semanticweb.owlapi.model.OWLAnnotationProperty |
date |
protected org.semanticweb.owlapi.model.OWLObjectProperty |
enabledBy |
protected org.semanticweb.owlapi.model.OWLAnnotationProperty |
evidence |
protected SimpleEcoMapper |
mapper |
protected org.semanticweb.owlapi.model.OWLClass |
mf |
protected Set<org.semanticweb.owlapi.model.OWLClass> |
mfSet |
protected org.semanticweb.owlapi.model.OWLObjectProperty |
occursIn |
protected org.semanticweb.owlapi.model.OWLObjectProperty |
partOf |
protected org.semanticweb.owlapi.model.OWLAnnotationProperty |
source |
Constructor and Description |
---|
LegoToGeneAnnotationTranslator(OWLGraphWrapper graph,
org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
SimpleEcoMapper mapper) |
Modifier and Type | Method and Description |
---|---|
protected void |
addAnnotations(OWLGraphWrapper modelGraph,
owltools.gaf.lego.legacy.AbstractLegoTranslator.Summary summary,
GafDocument annotations,
BioentityDocument entities) |
protected GeneAnnotation |
createAnnotation(AbstractLegoTranslator.Entry<org.semanticweb.owlapi.model.OWLClass> e,
Bioentity entity,
String Aspect,
OWLGraphWrapper g,
Collection<org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom> c16) |
protected Bioentity |
createBioentity(org.semanticweb.owlapi.model.OWLClass entityCls,
String entityType,
String taxon,
OWLGraphWrapper g) |
protected static Set<org.semanticweb.owlapi.model.OWLClass> |
getAllSubClasses(org.semanticweb.owlapi.model.OWLClass cls,
OWLGraphWrapper g,
org.semanticweb.owlapi.reasoner.OWLReasoner r,
boolean reflexive) |
protected AbstractLegoTranslator.BioentityStrings |
getBioentityStrings(org.semanticweb.owlapi.model.OWLClass entityCls,
String entityType,
String taxon,
OWLGraphWrapper g) |
protected String |
getEntityTaxon(org.semanticweb.owlapi.model.OWLClass entity,
org.semanticweb.owlapi.model.OWLNamedIndividual individual,
OWLGraphWrapper modelGraph) |
protected String |
getEntityType(org.semanticweb.owlapi.model.OWLClass entity,
OWLGraphWrapper modelGraph)
Get the type of an enabled by entity, e.g.
|
protected String |
getRelId(org.semanticweb.owlapi.model.OWLObjectPropertyExpression p,
OWLGraphWrapper graph) |
protected boolean |
isBp(org.semanticweb.owlapi.model.OWLClass cls) |
protected boolean |
isCc(org.semanticweb.owlapi.model.OWLClass cls) |
protected boolean |
isMf(org.semanticweb.owlapi.model.OWLClass cls) |
void |
translate(org.semanticweb.owlapi.model.OWLOntology modelAbox,
GafDocument annotations,
BioentityDocument entities,
List<String> additionalRefs) |
org.apache.commons.lang3.tuple.Pair<GafDocument,BioentityDocument> |
translate(String id,
org.semanticweb.owlapi.model.OWLOntology modelAbox,
List<String> additionalReferences) |
protected final org.semanticweb.owlapi.model.OWLObjectProperty partOf
protected final org.semanticweb.owlapi.model.OWLObjectProperty occursIn
protected final org.semanticweb.owlapi.model.OWLObjectProperty enabledBy
protected final org.semanticweb.owlapi.model.OWLAnnotationProperty source
protected final org.semanticweb.owlapi.model.OWLAnnotationProperty contributor
protected final org.semanticweb.owlapi.model.OWLAnnotationProperty date
protected final org.semanticweb.owlapi.model.OWLAnnotationProperty evidence
protected final org.semanticweb.owlapi.model.OWLClass mf
protected final Set<org.semanticweb.owlapi.model.OWLClass> mfSet
protected final org.semanticweb.owlapi.model.OWLClass cc
protected final Set<org.semanticweb.owlapi.model.OWLClass> ccSet
protected final org.semanticweb.owlapi.model.OWLClass bp
protected final Set<org.semanticweb.owlapi.model.OWLClass> bpSet
protected final SimpleEcoMapper mapper
public LegoToGeneAnnotationTranslator(OWLGraphWrapper graph, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, SimpleEcoMapper mapper)
public void translate(org.semanticweb.owlapi.model.OWLOntology modelAbox, GafDocument annotations, BioentityDocument entities, List<String> additionalRefs)
protected static Set<org.semanticweb.owlapi.model.OWLClass> getAllSubClasses(org.semanticweb.owlapi.model.OWLClass cls, OWLGraphWrapper g, org.semanticweb.owlapi.reasoner.OWLReasoner r, boolean reflexive)
protected boolean isMf(org.semanticweb.owlapi.model.OWLClass cls)
protected boolean isBp(org.semanticweb.owlapi.model.OWLClass cls)
protected boolean isCc(org.semanticweb.owlapi.model.OWLClass cls)
protected String getEntityType(org.semanticweb.owlapi.model.OWLClass entity, OWLGraphWrapper modelGraph)
modelGraph
- entity
- protected String getEntityTaxon(org.semanticweb.owlapi.model.OWLClass entity, org.semanticweb.owlapi.model.OWLNamedIndividual individual, OWLGraphWrapper modelGraph)
public org.apache.commons.lang3.tuple.Pair<GafDocument,BioentityDocument> translate(String id, org.semanticweb.owlapi.model.OWLOntology modelAbox, List<String> additionalReferences)
protected GeneAnnotation createAnnotation(AbstractLegoTranslator.Entry<org.semanticweb.owlapi.model.OWLClass> e, Bioentity entity, String Aspect, OWLGraphWrapper g, Collection<org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom> c16)
protected String getRelId(org.semanticweb.owlapi.model.OWLObjectPropertyExpression p, OWLGraphWrapper graph)
protected Bioentity createBioentity(org.semanticweb.owlapi.model.OWLClass entityCls, String entityType, String taxon, OWLGraphWrapper g)
protected AbstractLegoTranslator.BioentityStrings getBioentityStrings(org.semanticweb.owlapi.model.OWLClass entityCls, String entityType, String taxon, OWLGraphWrapper g)
protected void addAnnotations(OWLGraphWrapper modelGraph, owltools.gaf.lego.legacy.AbstractLegoTranslator.Summary summary, GafDocument annotations, BioentityDocument entities)
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