@Deprecated public class EcoTools extends Object
Constructor and Description |
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EcoTools(OWLGraphWrapper eco)
Deprecated.
Create a new instance using the ECO graph wrapper.
|
EcoTools(OWLGraphWrapper graph,
org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
boolean disposeReasoner)
Deprecated.
Create an instance for the given graph and reasoner.
|
EcoTools(ParserWrapper pw)
Deprecated.
Create a new instance using the given
ParserWrapper to load the ECO. |
Modifier and Type | Method and Description |
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void |
dispose()
Deprecated.
Clean up the internal data structures, usually done as last operation.
|
Set<org.semanticweb.owlapi.model.OWLClass> |
getAncestors(Set<org.semanticweb.owlapi.model.OWLClass> sources,
boolean reflexive)
Deprecated.
Wrapper method for the reasoner.
|
Set<org.semanticweb.owlapi.model.OWLClass> |
getClassesForGoCode(String goCode)
Deprecated.
Retrieve the ECO classes for the given GO annotation codes.
|
static Set<org.semanticweb.owlapi.model.OWLClass> |
getClassesForGoCodes(OWLGraphWrapper eco,
Set<String> goCodes)
Deprecated.
Retrieve the ECO classes for the given GO annotation codes.
|
static Set<org.semanticweb.owlapi.model.OWLClass> |
getClassesForGoCodes(OWLGraphWrapper eco,
String... goCodes)
Deprecated.
Retrieve the ECO classes for the given GO annotation codes.
|
static Set<String> |
getCodes(Set<org.semanticweb.owlapi.model.OWLClass> classes,
OWLGraphWrapper eco)
Deprecated.
|
static Set<String> |
getCodes(Set<org.semanticweb.owlapi.model.OWLClass> classes,
OWLGraphWrapper eco,
boolean includeDescendants)
Deprecated.
Retrieve the set of codes for a given set of ECO classes.
|
Set<org.semanticweb.owlapi.model.OWLClass> |
getDescendents(Set<org.semanticweb.owlapi.model.OWLClass> sources,
boolean reflexive)
Deprecated.
Wrapper method for the reasoner
|
static OWLGraphWrapper |
loadECO(ParserWrapper pw)
Deprecated.
Load the evidence code ontology (ECO) from its default PURL.
|
public static final String ECO_PURL
public EcoTools(OWLGraphWrapper graph, org.semanticweb.owlapi.reasoner.OWLReasoner reasoner, boolean disposeReasoner) throws org.semanticweb.owlapi.model.UnknownOWLOntologyException, org.semanticweb.owlapi.model.OWLOntologyCreationException
graph
- reasoner
- disposeReasoner
- set to true, if the reasoner should also be disposedorg.semanticweb.owlapi.model.UnknownOWLOntologyException
org.semanticweb.owlapi.model.OWLOntologyCreationException
dispose()
public EcoTools(ParserWrapper pw) throws org.semanticweb.owlapi.model.OWLOntologyCreationException, IOException, org.obolibrary.oboformat.parser.OBOFormatParserException
ParserWrapper
to load the ECO.pw
- org.semanticweb.owlapi.model.OWLOntologyCreationException
IOException
org.obolibrary.oboformat.parser.OBOFormatParserException
public EcoTools(OWLGraphWrapper eco)
eco
- public Set<org.semanticweb.owlapi.model.OWLClass> getClassesForGoCode(String goCode)
goCode
- public Set<org.semanticweb.owlapi.model.OWLClass> getAncestors(Set<org.semanticweb.owlapi.model.OWLClass> sources, boolean reflexive)
sources
- reflexive
- public Set<org.semanticweb.owlapi.model.OWLClass> getDescendents(Set<org.semanticweb.owlapi.model.OWLClass> sources, boolean reflexive)
sources
- reflexive
- public void dispose()
public static OWLGraphWrapper loadECO(ParserWrapper pw) throws IOException, org.semanticweb.owlapi.model.OWLOntologyCreationException, org.obolibrary.oboformat.parser.OBOFormatParserException
pw
- IOException
org.semanticweb.owlapi.model.OWLOntologyCreationException
org.obolibrary.oboformat.parser.OBOFormatParserException
public static Set<org.semanticweb.owlapi.model.OWLClass> getClassesForGoCodes(OWLGraphWrapper eco, String... goCodes)
eco
- goCodes
- public static Set<org.semanticweb.owlapi.model.OWLClass> getClassesForGoCodes(OWLGraphWrapper eco, Set<String> goCodes)
eco
- goCodes
- public static Set<String> getCodes(Set<org.semanticweb.owlapi.model.OWLClass> classes, OWLGraphWrapper eco)
public static Set<String> getCodes(Set<org.semanticweb.owlapi.model.OWLClass> classes, OWLGraphWrapper eco, boolean includeDescendants)
classes
- eco
- includeDescendants
- set to true if sub classes should be includedCopyright © 2010–2015. All rights reserved.