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GafDocument
or GeneAnnotation
.XMLStreamWriter
.Bioentity
object to the document.
MolecularModelManager.addEnabledBy(String, OWLNamedIndividual, OWLClassExpression)
MolecularModelManager.addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set)
MolecularModelManager.addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set)
MolecularModelManager.addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set)
MolecularModelManager.addFact(String, OWLObjectPropertyExpression, OWLNamedIndividual, OWLNamedIndividual, Set)
QuestForOrthologsSeqXMLParser.ProteinListener
.
QuestForOrthologsSeqXMLParser.MoreInfoProteinListener
.
MolecularModelManager.addOccursIn(String, OWLNamedIndividual, OWLClassExpression)
MolecularModelManager.addPartOf(String, OWLNamedIndividual, OWLNamedIndividual, Set)
MolecularModelManager.addType(String, OWLNamedIndividual, OWLClass)
MolecularModelManager.addType(String, OWLNamedIndividual, OWLObjectPropertyExpression, OWLClassExpression)
AnnotationRulesEngine
.AnnotationRule
objects from the qc file.AnnotationRuleViolation.ViolationType
.
LegoModelGenerator.buildNetwork(OWLClass, Collection)
EcoMapper
.
EcoMapper
.
EcoMapper
.
EcoMapper
.
EcoMapper
.
MolecularModelManager.createIndividual(String, OWLClass)
MolecularModelManager.createIndividual(String, OWLClass)
InputStream
.
SimpleEcoMapper
with from the mapping loaded from
the PURL.
SimpleEcoMapper
with from the mapping loaded from
the given source.
TraversingEcoMapper
instance using a new
ParserWrapper
to load ECO.
TraversingEcoMapper
instance using the given
ParserWrapper
to load ECO.
TraversingEcoMapper
instance using the given
ParserWrapper
to load ECO from the given location.
TraversingEcoMapper
instance using the given
OWLGraphWrapper
.
EcoMapper
and TraversingEcoMapper
.EcoMapper
, TraversingEcoMapper
and EcoMapperFactory
.ParserWrapper
to load the ECO.
GafDocument
has been finished.
GafDocument
has been finished.
GafDocument
has been finished.
OWLOntologyFormat
.
OWLOntologyFormat
does not map every format!
GafDocument
a gaf file.GeneAnnotation
lines,
excluding any headers.MolecularModelManager.generateModel(OWLClass, String)
ElkReasoner
will not detect unsatisfiable
classes, which result from inverse_of object properties.Bioentity
objects.
Bioentity
object for the given id.
GafDocument
).
GeneAnnotation
Bioentity
id.
MolecularModelJsonRenderer.getId(org.semanticweb.owlapi.model.OWLNamedObject, owltools.graph.OWLGraphWrapper)
GafObjectsBuilder.getNextSplitDocument()
method stops calling next method of the GAFParser
and returns the GafDocument
object build with the number of rows
GafDocument
) and OWL.
GafDocument
in plan and OWL format, check for
possible new inferred annotations (Prediction
).
GafDocument
, find the set of violations using the rule
GafDocument
in OWL, find the set of violations using the rule
AnnotationRuleViolation.ViolationType
.
OWLGraphWrapper
.GafDocument
into an OWL representation of the LEGO model.
QuestForOrthologsSeqXMLParser
.QuestForOrthologsSeqXMLParser
.MolecularModelManager.removeType(String, OWLNamedIndividual, OWLClass)
GafDocument
into an OWL representation of the LEGO model.
GeneAnnotation
) into an OWL representation of the LEGO model.
GafDocument
.
ClassTaxonMatrix
using the default delimiter.
ClassTaxonMatrix
using the specified delimiter.
GeneAnnotation
.
GeneAnnotation
.
Bioentity
.
GafDocument
.
GafDocument
.
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