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java.lang.Objectowltools.gaf.EcoTools
public class EcoTools
Methods to simplify the work with the evidence code ontology (ECO).
Field Summary | |
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static String |
ECO_PURL
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Constructor Summary | |
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EcoTools(OWLGraphWrapper eco)
Create a new instance using the ECO graph wrapper. |
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EcoTools(OWLGraphWrapper graph,
org.semanticweb.owlapi.reasoner.OWLReasoner reasoner,
boolean disposeReasoner)
Create an instance for the given graph and reasoner. |
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EcoTools(ParserWrapper pw)
Create a new instance using the given ParserWrapper to load the ECO. |
Method Summary | |
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void |
dispose()
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)
Wrapper method for the reasoner. |
Set<org.semanticweb.owlapi.model.OWLClass> |
getClassesForGoCode(String goCode)
Retrieve the ECO classes for the given GO annotation codes. |
static Set<org.semanticweb.owlapi.model.OWLClass> |
getClassesForGoCodes(OWLGraphWrapper eco,
Set<String> goCodes)
Retrieve the ECO classes for the given GO annotation codes. |
static Set<org.semanticweb.owlapi.model.OWLClass> |
getClassesForGoCodes(OWLGraphWrapper eco,
String... goCodes)
Retrieve the ECO classes for the given GO annotation codes. |
static Set<String> |
getCodes(Set<org.semanticweb.owlapi.model.OWLClass> classes,
OWLGraphWrapper eco)
|
static Set<String> |
getCodes(Set<org.semanticweb.owlapi.model.OWLClass> classes,
OWLGraphWrapper eco,
boolean includeDescendants)
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)
Wrapper method for the reasoner |
static OWLGraphWrapper |
loadECO(ParserWrapper pw)
Load the evidence code ontology (ECO) from its default PURL. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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public static final String ECO_PURL
Constructor Detail |
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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 disposed
org.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
- Method Detail |
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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 included
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